rs658804
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001080463.2(DYNC2H1):āc.6711A>Cā(p.Arg2237=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000844 in 1,612,234 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 ). Synonymous variant affecting the same amino acid position (i.e. R2237R) has been classified as Benign.
Frequency
Consequence
NM_001080463.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYNC2H1 | NM_001080463.2 | c.6711A>C | p.Arg2237= | synonymous_variant | 42/90 | ENST00000650373.2 | |
DYNC2H1 | NM_001377.3 | c.6711A>C | p.Arg2237= | synonymous_variant | 42/89 | ENST00000375735.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYNC2H1 | ENST00000650373.2 | c.6711A>C | p.Arg2237= | synonymous_variant | 42/90 | NM_001080463.2 | A1 | ||
DYNC2H1 | ENST00000375735.7 | c.6711A>C | p.Arg2237= | synonymous_variant | 42/89 | 1 | NM_001377.3 | P3 | |
DYNC2H1 | ENST00000334267.11 | c.2205+51900A>C | intron_variant | 1 | |||||
DYNC2H1 | ENST00000649323.1 | c.*4256A>C | 3_prime_UTR_variant, NMD_transcript_variant | 40/51 |
Frequencies
GnomAD3 genomes ? AF: 0.0000528 AC: 8AN: 151584Hom.: 1 Cov.: 30
GnomAD3 exomes AF: 0.000141 AC: 35AN: 248044Hom.: 0 AF XY: 0.000186 AC XY: 25AN XY: 134522
GnomAD4 exome AF: 0.0000876 AC: 128AN: 1460532Hom.: 0 Cov.: 57 AF XY: 0.000138 AC XY: 100AN XY: 726542
GnomAD4 genome ? AF: 0.0000527 AC: 8AN: 151702Hom.: 1 Cov.: 30 AF XY: 0.0000810 AC XY: 6AN XY: 74100
ClinVar
Submissions by phenotype
Jeune thoracic dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at