chr11-103200102-C-A
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001080463.2(DYNC2H1):c.8145C>A(p.Tyr2715Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000484 in 1,590,520 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001080463.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYNC2H1 | NM_001080463.2 | c.8145C>A | p.Tyr2715Ter | stop_gained | 50/90 | ENST00000650373.2 | |
DYNC2H1 | NM_001377.3 | c.8145C>A | p.Tyr2715Ter | stop_gained | 50/89 | ENST00000375735.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYNC2H1 | ENST00000650373.2 | c.8145C>A | p.Tyr2715Ter | stop_gained | 50/90 | NM_001080463.2 | A1 | ||
DYNC2H1 | ENST00000375735.7 | c.8145C>A | p.Tyr2715Ter | stop_gained | 50/89 | 1 | NM_001377.3 | P3 | |
DYNC2H1 | ENST00000334267.11 | c.2205+65683C>A | intron_variant | 1 | |||||
DYNC2H1 | ENST00000649323.1 | c.*5669C>A | 3_prime_UTR_variant, NMD_transcript_variant | 48/51 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000321 AC: 7AN: 217958Hom.: 0 AF XY: 0.0000511 AC XY: 6AN XY: 117368
GnomAD4 exome AF: 0.0000501 AC: 72AN: 1438392Hom.: 0 Cov.: 30 AF XY: 0.0000533 AC XY: 38AN XY: 713088
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74314
ClinVar
Submissions by phenotype
Asphyxiating thoracic dystrophy 3 Pathogenic:2
Likely pathogenic, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | - | - - |
Pathogenic, no assertion criteria provided | research | Dan Cohn Lab, University Of California Los Angeles | Jun 01, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at