chr8-26624181-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBA1
The NM_001197293.3(DPYSL2):c.667G>A(p.Ala223Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.002 in 1,614,186 control chromosomes in the GnomAD database, including 111 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001197293.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPYSL2 | NM_001197293.3 | c.667G>A | p.Ala223Thr | missense_variant | 4/14 | ENST00000521913.7 | |
DPYSL2 | NM_001386.6 | c.352G>A | p.Ala118Thr | missense_variant | 4/14 | ||
DPYSL2 | NM_001244604.2 | c.244G>A | p.Ala82Thr | missense_variant | 4/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPYSL2 | ENST00000521913.7 | c.667G>A | p.Ala223Thr | missense_variant | 4/14 | 1 | NM_001197293.3 |
Frequencies
GnomAD3 genomes AF: 0.00283 AC: 430AN: 152180Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.00644 AC: 1620AN: 251410Hom.: 75 AF XY: 0.00605 AC XY: 822AN XY: 135866
GnomAD4 exome AF: 0.00191 AC: 2791AN: 1461888Hom.: 98 Cov.: 29 AF XY: 0.00190 AC XY: 1379AN XY: 727246
GnomAD4 genome AF: 0.00282 AC: 430AN: 152298Hom.: 13 Cov.: 32 AF XY: 0.00333 AC XY: 248AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at