7-71132958-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022479.3(GALNT17):c.156C>A(p.Ser52Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,609,822 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022479.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALNT17 | NM_022479.3 | c.156C>A | p.Ser52Arg | missense_variant | Exon 1 of 11 | ENST00000333538.10 | NP_071924.1 | |
GALNT17 | XM_011516467.4 | c.156C>A | p.Ser52Arg | missense_variant | Exon 1 of 10 | XP_011514769.1 | ||
GALNT17 | XM_017012521.3 | c.156C>A | p.Ser52Arg | missense_variant | Exon 1 of 7 | XP_016868010.1 | ||
GALNT17 | XM_011516469.4 | c.156C>A | p.Ser52Arg | missense_variant | Exon 1 of 6 | XP_011514771.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000418 AC: 1AN: 239340Hom.: 0 AF XY: 0.00000764 AC XY: 1AN XY: 130934
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457676Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 725322
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.156C>A (p.S52R) alteration is located in exon 1 (coding exon 1) of the WBSCR17 gene. This alteration results from a C to A substitution at nucleotide position 156, causing the serine (S) at amino acid position 52 to be replaced by an arginine (R). 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