12-108789000-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_018984.4(SSH1):c.2138C>T(p.Pro713Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000168 in 1,609,928 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_018984.4 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 |
---|---|---|---|---|---|---|---|
SSH1 | NM_018984.4 | c.2138C>T | p.Pro713Leu | missense_variant | 15/15 | ENST00000326495.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SSH1 | ENST00000326495.10 | c.2138C>T | p.Pro713Leu | missense_variant | 15/15 | 1 | NM_018984.4 | P2 | |
SSH1 | ENST00000546433.5 | c.*1131C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151842Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249750Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135032
GnomAD4 exome AF: 0.0000158 AC: 23AN: 1458086Hom.: 0 Cov.: 33 AF XY: 0.0000152 AC XY: 11AN XY: 724824
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151842Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74148
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | 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