10-48725920-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001394531.1(WDFY4):āc.631G>Cā(p.Gly211Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000387 in 1,550,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001394531.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDFY4 | NM_001394531.1 | c.631G>C | p.Gly211Arg | missense_variant | 6/62 | ENST00000325239.12 | NP_001381460.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDFY4 | ENST00000325239.12 | c.631G>C | p.Gly211Arg | missense_variant | 6/62 | 5 | NM_001394531.1 | ENSP00000320563 | P1 | |
WDFY4 | ENST00000360890.6 | c.631G>C | p.Gly211Arg | missense_variant | 6/11 | 1 | ENSP00000354141 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000639 AC: 1AN: 156438Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82910
GnomAD4 exome AF: 0.00000358 AC: 5AN: 1398580Hom.: 0 Cov.: 30 AF XY: 0.00000435 AC XY: 3AN XY: 689598
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 07, 2022 | The c.631G>C (p.G211R) alteration is located in exon 6 (coding exon 5) of the WDFY4 gene. This alteration results from a G to C substitution at nucleotide position 631, causing the glycine (G) at amino acid position 211 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