NM_007086.4:c.2946A>T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007086.4(WDHD1):c.2946A>T(p.Arg982Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000316 in 1,584,772 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDHD1 | NM_007086.4 | c.2946A>T | p.Arg982Ser | missense_variant | Exon 24 of 26 | ENST00000360586.8 | NP_009017.1 | |
WDHD1 | NM_001008396.3 | c.2577A>T | p.Arg859Ser | missense_variant | Exon 23 of 25 | NP_001008397.1 | ||
WDHD1 | XM_006720012.2 | c.2940A>T | p.Arg980Ser | missense_variant | Exon 24 of 26 | XP_006720075.1 | ||
WDHD1 | XM_011536373.3 | c.1857A>T | p.Arg619Ser | missense_variant | Exon 15 of 17 | XP_011534675.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDHD1 | ENST00000360586.8 | c.2946A>T | p.Arg982Ser | missense_variant | Exon 24 of 26 | 1 | NM_007086.4 | ENSP00000353793.3 | ||
WDHD1 | ENST00000420358.2 | c.2577A>T | p.Arg859Ser | missense_variant | Exon 23 of 25 | 5 | ENSP00000399349.2 | |||
WDHD1 | ENST00000567693.1 | n.*1396A>T | non_coding_transcript_exon_variant | Exon 12 of 14 | 2 | ENSP00000456806.1 | ||||
WDHD1 | ENST00000567693.1 | n.*1396A>T | 3_prime_UTR_variant | Exon 12 of 14 | 2 | ENSP00000456806.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000443 AC: 1AN: 225534Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 122844
GnomAD4 exome AF: 0.00000279 AC: 4AN: 1432642Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 712694
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2946A>T (p.R982S) alteration is located in exon 24 (coding exon 23) of the WDHD1 gene. This alteration results from a A to T substitution at nucleotide position 2946, causing the arginine (R) at amino acid position 982 to be replaced by a serine (S). 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