chr17-29631410-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001282129.2(SSH2):c.3784G>T(p.Ala1262Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000595 in 1,614,038 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_001282129.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251294Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135852
GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.0000564 AC XY: 41AN XY: 727248
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3703G>T (p.A1235S) alteration is located in exon 15 (coding exon 15) of the SSH2 gene. This alteration results from a G to T substitution at nucleotide position 3703, causing the alanine (A) at amino acid position 1235 to be replaced by a serine (S). 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