11-103321208-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001080463.2(DYNC2H1):c.11926G>A(p.Val3976Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000165 in 1,609,654 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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. V3976V) has been classified as Likely benign.
Frequency
Consequence
NM_001080463.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYNC2H1 | NM_001080463.2 | c.11926G>A | p.Val3976Ile | missense_variant | 82/90 | ENST00000650373.2 | |
DYNC2H1 | NM_001377.3 | c.11905G>A | p.Val3969Ile | missense_variant | 81/89 | ENST00000375735.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYNC2H1 | ENST00000650373.2 | c.11926G>A | p.Val3976Ile | missense_variant | 82/90 | NM_001080463.2 | A1 | ||
DYNC2H1 | ENST00000375735.7 | c.11905G>A | p.Val3969Ile | missense_variant | 81/89 | 1 | NM_001377.3 | P3 | |
DYNC2H1 | ENST00000334267.11 | c.2206-114735G>A | intron_variant | 1 | |||||
DYNC2H1 | ENST00000528670.5 | c.1084G>A | p.Val362Ile | missense_variant, NMD_transcript_variant | 9/17 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000783 AC: 119AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000260 AC: 63AN: 242168Hom.: 1 AF XY: 0.000183 AC XY: 24AN XY: 131012
GnomAD4 exome AF: 0.000101 AC: 147AN: 1457474Hom.: 1 Cov.: 32 AF XY: 0.0000925 AC XY: 67AN XY: 724532
GnomAD4 genome AF: 0.000782 AC: 119AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.000685 AC XY: 51AN XY: 74402
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 14, 2017 | - - |
Asphyxiating thoracic dystrophy 3 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 13, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Jeune thoracic dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Intellectual disability Benign:1
Likely benign, no assertion criteria provided | clinical testing | Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille | Jan 01, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at