11-103209902-A-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BP7
The NM_001080463.2(DYNC2H1):c.8481A>C(p.Thr2827=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0023 in 1,495,460 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T2827T) has been classified as Likely benign.
Frequency
Consequence
NM_001080463.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYNC2H1 | NM_001080463.2 | c.8481A>C | p.Thr2827= | synonymous_variant | 53/90 | ENST00000650373.2 | |
DYNC2H1 | NM_001377.3 | c.8481A>C | p.Thr2827= | synonymous_variant | 53/89 | ENST00000375735.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYNC2H1 | ENST00000650373.2 | c.8481A>C | p.Thr2827= | synonymous_variant | 53/90 | NM_001080463.2 | A1 | ||
DYNC2H1 | ENST00000375735.7 | c.8481A>C | p.Thr2827= | synonymous_variant | 53/89 | 1 | NM_001377.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00126 AC: 191AN: 151992Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000741 AC: 92AN: 124198Hom.: 1 AF XY: 0.000636 AC XY: 42AN XY: 66074
GnomAD4 exome AF: 0.00242 AC: 3247AN: 1343350Hom.: 8 Cov.: 27 AF XY: 0.00235 AC XY: 1554AN XY: 661668
GnomAD4 genome ? AF: 0.00126 AC: 191AN: 152110Hom.: 1 Cov.: 32 AF XY: 0.00110 AC XY: 82AN XY: 74364
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 31, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 23, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | DYNC2H1: BP4, BP7 - |
Asphyxiating thoracic dystrophy 3 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 28, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Jeune thoracic dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at