11-103287549-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001377.3(DYNC2H1):c.11039C>T(p.Ala3680Val) variant causes a missense change. The variant allele was found at a frequency of 0.346 in 1,603,654 control chromosomes in the GnomAD database, including 98,755 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in ClinVar.
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 |
---|---|---|---|---|---|---|---|---|
DYNC2H1 | NM_001080463.2 | c.11060C>T | p.Ala3687Val | missense_variant | Exon 76 of 90 | ENST00000650373.2 | NP_001073932.1 | |
DYNC2H1 | NM_001377.3 | c.11039C>T | p.Ala3680Val | missense_variant | Exon 75 of 89 | ENST00000375735.7 | NP_001368.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DYNC2H1 | ENST00000650373.2 | c.11060C>T | p.Ala3687Val | missense_variant | Exon 76 of 90 | NM_001080463.2 | ENSP00000497174.1 | |||
DYNC2H1 | ENST00000375735.7 | c.11039C>T | p.Ala3680Val | missense_variant | Exon 75 of 89 | 1 | NM_001377.3 | ENSP00000364887.2 |
Frequencies
GnomAD3 genomes AF: 0.301 AC: 45696AN: 151842Hom.: 7174 Cov.: 32
GnomAD3 exomes AF: 0.319 AC: 77790AN: 244088Hom.: 13042 AF XY: 0.328 AC XY: 43478AN XY: 132410
GnomAD4 exome AF: 0.351 AC: 509918AN: 1451694Hom.: 91575 Cov.: 32 AF XY: 0.353 AC XY: 254978AN XY: 721994
GnomAD4 genome AF: 0.301 AC: 45731AN: 151960Hom.: 7180 Cov.: 32 AF XY: 0.302 AC XY: 22429AN XY: 74282
ClinVar
Submissions by phenotype
not specified Benign:5
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 -
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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Asphyxiating thoracic dystrophy 3 Benign:3
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. -
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Jeune thoracic dystrophy Benign:2
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at