10-86453790-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_015045.5(WAPL):c.2699G>A(p.Arg900His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,226 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 (★).
Frequency
Consequence
NM_015045.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WAPL | ENST00000298767.10 | c.2699G>A | p.Arg900His | missense_variant | Exon 13 of 19 | 1 | NM_015045.5 | ENSP00000298767.4 | ||
WAPL | ENST00000372075.2 | c.557G>A | p.Arg186His | missense_variant | Exon 5 of 10 | 2 | ENSP00000361145.2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250434Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135292
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461068Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726742
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2699G>A (p.R900H) alteration is located in exon 13 (coding exon 12) of the WAPL gene. This alteration results from a G to A substitution at nucleotide position 2699, causing the arginine (R) at amino acid position 900 to be replaced by a histidine (H). 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