1-11501536-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.544G>A(p.Gly182Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 1,593,124 control chromosomes in the GnomAD database, including 285,773 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
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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.544G>A | p.Gly182Ser | missense_variant | 2/21 | ENST00000294484.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DISP3 | ENST00000294484.7 | c.544G>A | p.Gly182Ser | missense_variant | 2/21 | 1 | NM_020780.2 | P1 | |
ENST00000649975.1 | n.466+15C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.495 AC: 75230AN: 151976Hom.: 21349 Cov.: 33
GnomAD3 exomes AF: 0.549 AC: 125195AN: 228176Hom.: 37178 AF XY: 0.545 AC XY: 68162AN XY: 125054
GnomAD4 exome AF: 0.595 AC: 858021AN: 1441030Hom.: 264413 Cov.: 89 AF XY: 0.589 AC XY: 421066AN XY: 715172
GnomAD4 genome ? AF: 0.495 AC: 75254AN: 152094Hom.: 21360 Cov.: 33 AF XY: 0.491 AC XY: 36500AN XY: 74342
ClinVar
Submissions by phenotype
DISP3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 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