chrX-71224406-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BP7
The NM_000166.6(GJB1):c.699G>A(p.Ser233=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000091 in 1,208,254 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. S233S) has been classified as Likely benign.
Frequency
Consequence
NM_000166.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GJB1 | NM_000166.6 | c.699G>A | p.Ser233= | synonymous_variant | 2/2 | ENST00000361726.7 | |
GJB1 | NM_001097642.3 | c.699G>A | p.Ser233= | synonymous_variant | 2/2 | ||
GJB1 | XM_011530907.3 | c.699G>A | p.Ser233= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GJB1 | ENST00000361726.7 | c.699G>A | p.Ser233= | synonymous_variant | 2/2 | 1 | NM_000166.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111489Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 33689
GnomAD3 exomes AF: 0.0000112 AC: 2AN: 178217Hom.: 0 AF XY: 0.0000314 AC XY: 2AN XY: 63705
GnomAD4 exome AF: 0.00000821 AC: 9AN: 1096765Hom.: 0 Cov.: 32 AF XY: 0.00000276 AC XY: 1AN XY: 362265
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111489Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 33689
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Oct 13, 2016 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 11, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Charcot-Marie-Tooth Neuropathy X Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at