rs267608432
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_Very_StrongBP7BS2_Supporting
The NM_001110792.2(MECP2):c.189C>T(p.His63=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000455 in 1,097,987 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001110792.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MECP2 | NM_001110792.2 | c.189C>T | p.His63= | synonymous_variant | 2/3 | ENST00000453960.7 | |
MECP2 | NM_004992.4 | c.153C>T | p.His51= | synonymous_variant | 3/4 | ENST00000303391.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MECP2 | ENST00000453960.7 | c.189C>T | p.His63= | synonymous_variant | 2/3 | 1 | NM_001110792.2 | ||
MECP2 | ENST00000303391.11 | c.153C>T | p.His51= | synonymous_variant | 3/4 | 1 | NM_004992.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183080Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67596
GnomAD4 exome AF: 0.00000455 AC: 5AN: 1097987Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 2AN XY: 363349
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
Severe neonatal-onset encephalopathy with microcephaly Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 12, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at