chr13-36170584-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017826.3(SOHLH2):c.1204C>T(p.Arg402Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,614,054 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R402Q) has been classified as Likely benign.
Frequency
Consequence
NM_017826.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOHLH2 | NM_017826.3 | c.1204C>T | p.Arg402Trp | missense_variant | 10/11 | ENST00000379881.8 | |
CCDC169-SOHLH2 | NM_001198910.2 | c.1435C>T | p.Arg479Trp | missense_variant | 15/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOHLH2 | ENST00000379881.8 | c.1204C>T | p.Arg402Trp | missense_variant | 10/11 | 1 | NM_017826.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251328Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135824
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461870Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 20AN XY: 727238
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.1435C>T (p.R479W) alteration is located in exon 15 (coding exon 14) of the CCDC169-SOHLH2 gene. This alteration results from a C to T substitution at nucleotide position 1435, causing the arginine (R) at amino acid position 479 to be replaced by a tryptophan (W). 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