X-48601914-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001347217.2(WDR13):c.962C>T(p.Ala321Val) variant causes a missense change. The variant allele was found at a frequency of 0.00001 in 1,198,367 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001347217.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR13 | ENST00000376729.10 | c.962C>T | p.Ala321Val | missense_variant | Exon 7 of 10 | 5 | NM_001347217.2 | ENSP00000365919.5 | ||
WDR13 | ENST00000218056.9 | c.962C>T | p.Ala321Val | missense_variant | Exon 6 of 9 | 1 | ENSP00000218056.5 | |||
WDR13 | ENST00000479279.5 | n.1829C>T | non_coding_transcript_exon_variant | Exon 5 of 8 | 1 | |||||
WDR13 | ENST00000482760.3 | c.206C>T | p.Ala69Val | missense_variant | Exon 2 of 5 | 3 | ENSP00000483191.1 |
Frequencies
GnomAD3 genomes AF: 0.0000266 AC: 3AN: 112698Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34840
GnomAD4 exome AF: 0.00000829 AC: 9AN: 1085669Hom.: 0 Cov.: 31 AF XY: 0.0000142 AC XY: 5AN XY: 353061
GnomAD4 genome AF: 0.0000266 AC: 3AN: 112698Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34840
ClinVar
Submissions by phenotype
not provided Uncertain:2
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not specified Uncertain:1
The c.962C>T (p.A321V) alteration is located in exon 6 (coding exon 6) of the WDR13 gene. This alteration results from a C to T substitution at nucleotide position 962, causing the alanine (A) at amino acid position 321 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