13-36170583-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_017826.3(SOHLH2):c.1205G>A(p.Arg402Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0183 in 1,613,976 control chromosomes in the GnomAD database, including 348 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R402W) has been classified as Uncertain significance.
Frequency
Consequence
NM_017826.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SOHLH2 | ENST00000379881.8 | c.1205G>A | p.Arg402Gln | missense_variant | Exon 10 of 11 | 1 | NM_017826.3 | ENSP00000369210.3 | ||
CCDC169-SOHLH2 | ENST00000511166.1 | c.1436G>A | p.Arg479Gln | missense_variant | Exon 15 of 16 | 2 | ENSP00000421868.1 |
Frequencies
GnomAD3 genomes AF: 0.0146 AC: 2220AN: 151990Hom.: 26 Cov.: 32
GnomAD3 exomes AF: 0.0143 AC: 3599AN: 251308Hom.: 44 AF XY: 0.0145 AC XY: 1969AN XY: 135818
GnomAD4 exome AF: 0.0187 AC: 27327AN: 1461868Hom.: 322 Cov.: 30 AF XY: 0.0184 AC XY: 13357AN XY: 727232
GnomAD4 genome AF: 0.0146 AC: 2218AN: 152108Hom.: 26 Cov.: 32 AF XY: 0.0148 AC XY: 1099AN XY: 74340
ClinVar
Submissions by phenotype
CCDC169-SOHLH2-related disorder Benign:1
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at