Variant: NM_001110792.2(MECP2):c.414-3C>T

CA10558616

522665 (ClinVar)

Gene: MECP2

Condition: Rett syndrome

Inheritance Mode: X-linked inheritance

UUID: b85a7f87-970a-4713-8132-527d4b4713ec

HGVS expressions

NM_001110792.2:c.414-3C>T
NM_001110792.2(MECP2):c.414-3C>T
NC_000023.11:g.154031453G>A
CM000685.2:g.154031453G>A
NC_000023.10:g.153296904G>A
CM000685.1:g.153296904G>A
NC_000023.9:g.152950098G>A
NG_007107.2:g.110675C>T
NG_007107.3:g.110651C>T
ENST00000303391.11:c.378-3C>T
ENST00000453960.7:c.414-3C>T
ENST00000637917.1:n.11-3C>T
ENST00000303391.10:c.378-3C>T
ENST00000369957.5:c.*432-3C>T
ENST00000407218.5:c.414-3C>T
ENST00000453960.6:c.414-3C>T
ENST00000486506.5:n.2726-3C>T
ENST00000611468.1:c.366-3C>T
ENST00000619732.4:c.378-3C>T
ENST00000622433.4:c.366-3C>T
ENST00000628176.2:c.378-3C>T
NM_001110792.1:c.414-3C>T
NM_001316337.1:c.99-3C>T
NM_004992.3:c.378-3C>T
NM_001316337.2:c.99-3C>T
NM_001369391.2:c.99-3C>T
NM_001369392.2:c.99-3C>T
NM_001369393.2:c.99-3C>T
NM_001369394.1:c.99-3C>T
NM_001369394.2:c.99-3C>T
NM_001386137.1:c.-183-3C>T
NM_001386138.1:c.-183-3C>T
NM_001386139.1:c.-183-3C>T
NM_004992.4:c.378-3C>T

Benign

• Met criteria codes: BA1 BS2 BP5

• Not Met criteria codes: PP3

Expert Panel

Rett and Angelman-like Disorders VCEP

Criteria Specification Information

Evidence submitted by expert panel

Rett and Angelman-like Disorders VCEP

The c.378-3C>T variant in MECP2 (NM_004992.3) has an allele frequency of 0.038% in "Other" sub population in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1). The c.378-3C>T variant is observed in at least 2 unaffected individuals (Invitae internal database) (BS2). The c.378-3C>T variant is found in a patient with an alternate molecular basis of disease (Invitae internal database) (BP5). In summary, the c.378-3C>T variant in MECP2 is classified as benign for Rett Syndrome based on the ACMG/AMP criteria (BA1, BS2, BP5).

Met criteria codes

• BA1: The c.378-3C>T variant in MECP2 has an allele frequency of 0.038% in the Other sub population in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1).
• BS2: The c.378-3C>T variant is observed in at least 2 unaffected individuals (Invitae internal database).
• BP5: The c.378-3C>T variant is found in a patient with an alternate molecular basis of disease (Invitae internal database).

Not Met criteria codes

• PP3: Splicing prediction on this position does not support an impact (MaxEntScan, NNSPLICE, HumanspliceFinder)

Approved on: 2022-02-18

Published on: 2022-06-30