chr10-86452037-A-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_015045.5(WAPL):āc.3044T>Cā(p.Ile1015Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000867 in 1,614,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I1015V) has been classified as Uncertain significance.
Frequency
Consequence
NM_015045.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WAPL | NM_015045.5 | c.3044T>C | p.Ile1015Thr | missense_variant | 15/19 | ENST00000298767.10 | |
WAPL | NM_001318328.2 | c.3026T>C | p.Ile1009Thr | missense_variant | 15/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WAPL | ENST00000298767.10 | c.3044T>C | p.Ile1015Thr | missense_variant | 15/19 | 1 | NM_015045.5 | P1 | |
WAPL | ENST00000372075.2 | c.807+1183T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251476Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135912
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461876Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727240
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2023 | The c.3044T>C (p.I1015T) alteration is located in exon 15 (coding exon 14) of the WAPL gene. This alteration results from a T to C substitution at nucleotide position 3044, causing the isoleucine (I) at amino acid position 1015 to be replaced by a threonine (T). 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