16-25692422-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006040.3(HS3ST4):c.5C>T(p.Ala2Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000492 in 1,055,992 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 Uncertain significance (★).
Frequency
Consequence
NM_006040.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000826 AC: 12AN: 145352Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000224 AC: 1AN: 4472Hom.: 0 AF XY: 0.000374 AC XY: 1AN XY: 2674
GnomAD4 exome AF: 0.0000439 AC: 40AN: 910640Hom.: 0 Cov.: 14 AF XY: 0.0000459 AC XY: 20AN XY: 435456
GnomAD4 genome AF: 0.0000826 AC: 12AN: 145352Hom.: 0 Cov.: 31 AF XY: 0.0000566 AC XY: 4AN XY: 70724
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5C>T (p.A2V) alteration is located in exon 1 (coding exon 1) of the HS3ST4 gene. This alteration results from a C to T substitution at nucleotide position 5, causing the alanine (A) at amino acid position 2 to be replaced by a valine (V). 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