12-108788156-A-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_018984.4(SSH1):c.2982T>G(p.Ser994Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000221 in 1,613,926 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 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.2982T>G | p.Ser994Arg | missense_variant | 15/15 | ENST00000326495.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SSH1 | ENST00000326495.10 | c.2982T>G | p.Ser994Arg | missense_variant | 15/15 | 1 | NM_018984.4 | P2 | |
SSH1 | ENST00000546433.5 | c.*1975T>G | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00120 AC: 183AN: 151920Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000295 AC: 74AN: 251250Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135826
GnomAD4 exome AF: 0.000117 AC: 171AN: 1461888Hom.: 0 Cov.: 30 AF XY: 0.000110 AC XY: 80AN XY: 727248
GnomAD4 genome ? AF: 0.00122 AC: 185AN: 152038Hom.: 0 Cov.: 32 AF XY: 0.00109 AC XY: 81AN XY: 74328
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at