chr13-36190036-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_017826.3(SOHLH2):c.551G>A(p.Gly184Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000442 in 1,605,590 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_017826.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOHLH2 | NM_017826.3 | c.551G>A | p.Gly184Asp | missense_variant | 6/11 | ENST00000379881.8 | |
CCDC169-SOHLH2 | NM_001198910.2 | c.782G>A | p.Gly261Asp | missense_variant | 11/16 | ||
SOHLH2 | NM_001282147.2 | c.551G>A | p.Gly184Asp | missense_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOHLH2 | ENST00000379881.8 | c.551G>A | p.Gly184Asp | missense_variant | 6/11 | 1 | NM_017826.3 | P1 | |
SOHLH2 | ENST00000317764.6 | c.551G>A | p.Gly184Asp | missense_variant | 6/7 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000284 AC: 7AN: 246906Hom.: 0 AF XY: 0.0000374 AC XY: 5AN XY: 133550
GnomAD4 exome AF: 0.0000440 AC: 64AN: 1453512Hom.: 0 Cov.: 30 AF XY: 0.0000374 AC XY: 27AN XY: 722684
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74284
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at