Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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  • See Evidence submitted by expert panel for details.

Variant: NM_004992.3(MECP2):c.377+24C>A

CA199494

156055 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 43948ad9-89c0-470c-809c-721f238ab892

HGVS expressions

NM_004992.3:c.377+24C>A
NM_004992.3(MECP2):c.377+24C>A
NC_000023.11:g.154032183G>T
CM000685.2:g.154032183G>T
NC_000023.10:g.153297634G>T
CM000685.1:g.153297634G>T
NC_000023.9:g.152950828G>T
NG_007107.2:g.109945C>A
NG_007107.3:g.109921C>A
ENST00000303391.11:c.377+24C>A
ENST00000453960.7:c.413+24C>A
ENST00000637917.1:n.10+24C>A
ENST00000303391.10:c.377+24C>A
ENST00000369957.5:c.*431+24C>A
ENST00000407218.5:c.413+24C>A
ENST00000453960.6:c.413+24C>A
ENST00000486506.5:n.2725+24C>A
ENST00000611468.1:c.365+24C>A
ENST00000619732.4:c.377+24C>A
ENST00000622433.4:c.365+24C>A
ENST00000628176.2:c.377+24C>A
NM_001110792.1:c.413+24C>A
NM_001316337.1:c.98+24C>A
NM_001110792.2:c.413+24C>A
NM_001316337.2:c.98+24C>A
NM_001369391.2:c.98+24C>A
NM_001369392.2:c.98+24C>A
NM_001369393.2:c.98+24C>A
NM_001369394.1:c.98+24C>A
NM_001369394.2:c.98+24C>A
NM_001386137.1:c.-184+24C>A
NM_001386138.1:c.-184+24C>A
NM_001386139.1:c.-184+24C>A
NM_004992.4:c.377+24C>A
NM_001110792.2(MECP2):c.413+24C>A

Likely Benign

Met criteria codes 2
BS1 BP4
Not Met criteria codes 1
PP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Rett and Angelman-like Disorders VCEP
The allele frequency of the c.377+24C>A variant in MECP2 (NM_004992.3) is 0.01% in Latino/Admixed American sub population in gnomAD, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1). Splice prediction analysis, using multiple computational tools does not suggest an impact to splicing (BP4). In summary, the c.377+24C>A variant in MECP2 is classified as Likely Benign based on the ACMG/AMP criteria (BS1, BP4).
Met criteria codes
BS1
The allele frequency of the c.377+24C>A variant in MECP2 is 0.01% in Latino/Admixed American sub population in gnomAD, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1).
BP4
Splice prediction analysis, using multiple computational tools does not suggest an impact to splicing (BP4).
Not Met criteria codes
PP4
The c.377+24C>A variant was identified in a male with non-specific intellectual disabilities (PMID 17084570).
Approved on: 2021-10-26
Published on: 2021-12-27
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