2-72179342-T-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_015189.3(EXOC6B):c.2429A>G(p.His810Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0024 in 1,607,554 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H810Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_015189.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EXOC6B | NM_015189.3 | c.2429A>G | p.His810Arg | missense_variant | 22/22 | ENST00000272427.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EXOC6B | ENST00000272427.11 | c.2429A>G | p.His810Arg | missense_variant | 22/22 | 1 | NM_015189.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00189 AC: 287AN: 151924Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00193 AC: 465AN: 240808Hom.: 2 AF XY: 0.00196 AC XY: 256AN XY: 130740
GnomAD4 exome AF: 0.00246 AC: 3576AN: 1455510Hom.: 6 Cov.: 31 AF XY: 0.00239 AC XY: 1729AN XY: 723472
GnomAD4 genome ? AF: 0.00189 AC: 287AN: 152044Hom.: 0 Cov.: 32 AF XY: 0.00187 AC XY: 139AN XY: 74326
ClinVar
Submissions by phenotype
EXOC6B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 24, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at