chr13-36189998-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017826.3(SOHLH2):c.589G>A(p.Glu197Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,606,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017826.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOHLH2 | NM_017826.3 | c.589G>A | p.Glu197Lys | missense_variant | 6/11 | ENST00000379881.8 | |
CCDC169-SOHLH2 | NM_001198910.2 | c.820G>A | p.Glu274Lys | missense_variant | 11/16 | ||
SOHLH2 | NM_001282147.2 | c.589G>A | p.Glu197Lys | missense_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOHLH2 | ENST00000379881.8 | c.589G>A | p.Glu197Lys | missense_variant | 6/11 | 1 | NM_017826.3 | P1 | |
SOHLH2 | ENST00000317764.6 | c.589G>A | p.Glu197Lys | missense_variant | 6/7 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152062Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 247920Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 134154
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1454708Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 723516
GnomAD4 genome AF: 0.0000658 AC: 10AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 12, 2024 | The c.820G>A (p.E274K) alteration is located in exon 11 (coding exon 10) of the CCDC169-SOHLH2 gene. This alteration results from a G to A substitution at nucleotide position 820, causing the glutamic acid (E) at amino acid position 274 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at