rs589623
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001377.3(DYNC2H1):c.8612G>A(p.Arg2871Gln) variant causes a missense change. The variant allele was found at a frequency of 0.793 in 1,521,494 control chromosomes in the GnomAD database, including 480,082 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001377.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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DYNC2H1 | NM_001080463.2 | c.8612G>A | p.Arg2871Gln | missense_variant | Exon 54 of 90 | ENST00000650373.2 | NP_001073932.1 | |
DYNC2H1 | NM_001377.3 | c.8612G>A | p.Arg2871Gln | missense_variant | Exon 54 of 89 | ENST00000375735.7 | NP_001368.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DYNC2H1 | ENST00000650373.2 | c.8612G>A | p.Arg2871Gln | missense_variant | Exon 54 of 90 | NM_001080463.2 | ENSP00000497174.1 | |||
DYNC2H1 | ENST00000375735.7 | c.8612G>A | p.Arg2871Gln | missense_variant | Exon 54 of 89 | 1 | NM_001377.3 | ENSP00000364887.2 | ||
DYNC2H1 | ENST00000334267.11 | c.2205+77442G>A | intron_variant | Intron 15 of 19 | 1 | ENSP00000334021.7 | ||||
DYNC2H1 | ENST00000533027.1 | n.212G>A | non_coding_transcript_exon_variant | Exon 3 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.756 AC: 114756AN: 151872Hom.: 43869 Cov.: 32
GnomAD3 exomes AF: 0.794 AC: 120667AN: 152026Hom.: 48240 AF XY: 0.795 AC XY: 63767AN XY: 80228
GnomAD4 exome AF: 0.797 AC: 1091217AN: 1369504Hom.: 436169 Cov.: 32 AF XY: 0.796 AC XY: 537112AN XY: 674624
GnomAD4 genome AF: 0.756 AC: 114855AN: 151990Hom.: 43913 Cov.: 32 AF XY: 0.756 AC XY: 56184AN XY: 74278
ClinVar
Submissions by phenotype
not specified Benign:5
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
Asphyxiating thoracic dystrophy 3 Benign:3
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
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Jeune thoracic dystrophy Benign:1
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Short rib-polydactyly syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at