chr12-108789042-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018984.4(SSH1):c.2096G>A(p.Arg699His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000454 in 1,608,946 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 Uncertain significance (★).
Frequency
Consequence
NM_018984.4 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 |
---|---|---|---|---|---|---|---|
SSH1 | NM_018984.4 | c.2096G>A | p.Arg699His | missense_variant | 15/15 | ENST00000326495.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SSH1 | ENST00000326495.10 | c.2096G>A | p.Arg699His | missense_variant | 15/15 | 1 | NM_018984.4 | P2 | |
SSH1 | ENST00000546433.5 | c.*1089G>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151942Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000882 AC: 22AN: 249432Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 134784
GnomAD4 exome AF: 0.0000494 AC: 72AN: 1457004Hom.: 0 Cov.: 33 AF XY: 0.0000566 AC XY: 41AN XY: 723954
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151942Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74198
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 2023 | The c.2096G>A (p.R699H) alteration is located in exon 15 (coding exon 15) of the SSH1 gene. This alteration results from a G to A substitution at nucleotide position 2096, causing the arginine (R) at amino acid position 699 to be replaced by a histidine (H). 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