10-116915404-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001127211.3(SHTN1):c.1276G>A(p.Val426Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000149 in 1,605,582 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_001127211.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251074Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135708
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1453398Hom.: 0 Cov.: 27 AF XY: 0.0000193 AC XY: 14AN XY: 723700
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1276G>A (p.V426I) alteration is located in exon 13 (coding exon 13) of the SHTN1 gene. This alteration results from a G to A substitution at nucleotide position 1276, causing the valine (V) at amino acid position 426 to be replaced by an isoleucine (I). 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