12-108788422-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018984.4(SSH1):c.2716G>A(p.Asp906Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000251 in 1,596,268 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SSH1 | ENST00000326495.10 | c.2716G>A | p.Asp906Asn | missense_variant | Exon 15 of 15 | 1 | NM_018984.4 | ENSP00000315713.5 | ||
SSH1 | ENST00000546433.5 | n.*1709G>A | non_coding_transcript_exon_variant | Exon 7 of 7 | 5 | ENSP00000447629.1 | ||||
SSH1 | ENST00000546433.5 | n.*1709G>A | 3_prime_UTR_variant | Exon 7 of 7 | 5 | ENSP00000447629.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000858 AC: 2AN: 233064Hom.: 0 AF XY: 0.0000158 AC XY: 2AN XY: 126236
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1443994Hom.: 0 Cov.: 33 AF XY: 0.00000139 AC XY: 1AN XY: 717016
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2716G>A (p.D906N) 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 2716, causing the aspartic acid (D) at amino acid position 906 to be replaced by an asparagine (N). 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