rs368824340
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The ENST00000375735.7(DYNC2H1):āc.6918A>Gā(p.Ser2306=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000149 in 1,613,010 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. S2306S) has been classified as Likely benign.
Frequency
Consequence
ENST00000375735.7 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DYNC2H1 | NM_001080463.2 | c.6918A>G | p.Ser2306= | synonymous_variant | 43/90 | ENST00000650373.2 | NP_001073932.1 | |
DYNC2H1 | NM_001377.3 | c.6918A>G | p.Ser2306= | synonymous_variant | 43/89 | ENST00000375735.7 | NP_001368.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DYNC2H1 | ENST00000650373.2 | c.6918A>G | p.Ser2306= | synonymous_variant | 43/90 | NM_001080463.2 | ENSP00000497174 | A1 | ||
DYNC2H1 | ENST00000375735.7 | c.6918A>G | p.Ser2306= | synonymous_variant | 43/89 | 1 | NM_001377.3 | ENSP00000364887 | P3 | |
DYNC2H1 | ENST00000334267.11 | c.2205+52945A>G | intron_variant | 1 | ENSP00000334021 | |||||
DYNC2H1 | ENST00000649323.1 | c.*4463A>G | 3_prime_UTR_variant, NMD_transcript_variant | 41/51 | ENSP00000497581 |
Frequencies
GnomAD3 genomes AF: 0.000921 AC: 140AN: 152044Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000189 AC: 47AN: 248498Hom.: 0 AF XY: 0.000119 AC XY: 16AN XY: 134802
GnomAD4 exome AF: 0.0000678 AC: 99AN: 1460848Hom.: 0 Cov.: 30 AF XY: 0.0000537 AC XY: 39AN XY: 726700
GnomAD4 genome AF: 0.000933 AC: 142AN: 152162Hom.: 1 Cov.: 32 AF XY: 0.000914 AC XY: 68AN XY: 74386
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 28, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 17, 2020 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Mar 25, 2018 | The c.6918A>G; p.Ser2306Ser variant (rs368824340, ClinVar variant ID 281774) does not alter the amino acid sequence of the DYNC2H1 protein and computational splice site prediction algorithms do not predict a change in the nearest splice site or creation of a cryptic splice site. This variant has not been reported in association with skeletal dysplasia in medical literature or in gene specific variation databases. This variant is listed in the genome Aggregation Database (gnomAD) with an African population frequency of 0.3% (identified on 75 out of 23,996 chromosomes). Based on the available information, the c.6918A>G variant is likely to be benign. - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 10, 2018 | - - |
DYNC2H1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 12, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Jeune thoracic dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 16, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at