chr7-71710860-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022479.3(GALNT17):c.1600C>T(p.Arg534Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000322 in 1,613,788 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R534Q) has been classified 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNT17 | NM_022479.3 | c.1600C>T | p.Arg534Trp | missense_variant | 10/11 | ENST00000333538.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNT17 | ENST00000333538.10 | c.1600C>T | p.Arg534Trp | missense_variant | 10/11 | 1 | NM_022479.3 | P1 | |
GALNT17 | ENST00000467723.1 | n.1534C>T | non_coding_transcript_exon_variant | 10/11 | 2 | ||||
GALNT17 | ENST00000498380.6 | n.2002C>T | non_coding_transcript_exon_variant | 10/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251242Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135838
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461600Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 727098
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2021 | The c.1600C>T (p.R534W) alteration is located in exon 10 (coding exon 10) of the WBSCR17 gene. This alteration results from a C to T substitution at nucleotide position 1600, causing the arginine (R) at amino acid position 534 to be replaced by a tryptophan (W). 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