14-54962779-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007086.4(WDHD1):c.2606G>A(p.Gly869Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,613,716 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007086.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDHD1 | NM_007086.4 | c.2606G>A | p.Gly869Glu | missense_variant | Exon 20 of 26 | ENST00000360586.8 | NP_009017.1 | |
WDHD1 | NM_001008396.3 | c.2237G>A | p.Gly746Glu | missense_variant | Exon 19 of 25 | NP_001008397.1 | ||
WDHD1 | XM_006720012.2 | c.2606G>A | p.Gly869Glu | missense_variant | Exon 20 of 26 | XP_006720075.1 | ||
WDHD1 | XM_011536373.3 | c.1517G>A | p.Gly506Glu | missense_variant | Exon 11 of 17 | XP_011534675.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDHD1 | ENST00000360586.8 | c.2606G>A | p.Gly869Glu | missense_variant | Exon 20 of 26 | 1 | NM_007086.4 | ENSP00000353793.3 | ||
WDHD1 | ENST00000420358.2 | c.2237G>A | p.Gly746Glu | missense_variant | Exon 19 of 25 | 5 | ENSP00000399349.2 | |||
WDHD1 | ENST00000567693.1 | n.*1056G>A | non_coding_transcript_exon_variant | Exon 8 of 14 | 2 | ENSP00000456806.1 | ||||
WDHD1 | ENST00000567693.1 | n.*1056G>A | 3_prime_UTR_variant | Exon 8 of 14 | 2 | ENSP00000456806.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251142Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135770
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461552Hom.: 0 Cov.: 33 AF XY: 0.0000248 AC XY: 18AN XY: 727066
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2606G>A (p.G869E) alteration is located in exon 20 (coding exon 19) of the WDHD1 gene. This alteration results from a G to A substitution at nucleotide position 2606, causing the glycine (G) at amino acid position 869 to be replaced by a glutamic acid (E). 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