1-11519413-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_020780.2(DISP3):c.1948G>A(p.Ala650Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 1,613,438 control chromosomes in the GnomAD database, including 287,725 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_020780.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DISP3 | NM_020780.2 | c.1948G>A | p.Ala650Thr | missense_variant | 8/21 | ENST00000294484.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DISP3 | ENST00000294484.7 | c.1948G>A | p.Ala650Thr | missense_variant | 8/21 | 1 | NM_020780.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.471 AC: 71608AN: 151894Hom.: 20735 Cov.: 32
GnomAD3 exomes AF: 0.555 AC: 138471AN: 249316Hom.: 42314 AF XY: 0.552 AC XY: 74741AN XY: 135280
GnomAD4 exome AF: 0.593 AC: 866949AN: 1461426Hom.: 266985 Cov.: 68 AF XY: 0.588 AC XY: 427632AN XY: 727030
GnomAD4 genome AF: 0.471 AC: 71624AN: 152012Hom.: 20740 Cov.: 32 AF XY: 0.470 AC XY: 34917AN XY: 74304
ClinVar
Submissions by phenotype
DISP3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 16, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at