chr1-11501143-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_020780.2(DISP3):c.151C>G(p.Leu51Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00108 in 1,613,926 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 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 -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DISP3 | NM_020780.2 | c.151C>G | p.Leu51Val | missense_variant | 2/21 | ENST00000294484.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DISP3 | ENST00000294484.7 | c.151C>G | p.Leu51Val | missense_variant | 2/21 | 1 | NM_020780.2 | P1 | |
ENST00000649975.1 | n.711G>C | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes ? AF: 0.00133 AC: 203AN: 152170Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00351 AC: 873AN: 248574Hom.: 9 AF XY: 0.00309 AC XY: 417AN XY: 134912
GnomAD4 exome AF: 0.00106 AC: 1547AN: 1461638Hom.: 15 Cov.: 31 AF XY: 0.00102 AC XY: 739AN XY: 727118
GnomAD4 genome ? AF: 0.00133 AC: 203AN: 152288Hom.: 4 Cov.: 32 AF XY: 0.00144 AC XY: 107AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
DISP3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 13, 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