chr3-52396681-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_015512.5(DNAH1):c.11494C>T(p.Arg3832Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00346 in 1,613,720 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R3832H) has been classified as Benign.
Frequency
Consequence
NM_015512.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH1 | NM_015512.5 | c.11494C>T | p.Arg3832Cys | missense_variant | 72/78 | ENST00000420323.7 | |
DNAH1 | XM_017006129.2 | c.11563C>T | p.Arg3855Cys | missense_variant | 74/80 | ||
DNAH1 | XM_017006130.2 | c.11494C>T | p.Arg3832Cys | missense_variant | 73/79 | ||
DNAH1 | XM_017006131.2 | c.11437C>T | p.Arg3813Cys | missense_variant | 73/79 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH1 | ENST00000420323.7 | c.11494C>T | p.Arg3832Cys | missense_variant | 72/78 | 1 | NM_015512.5 | P1 | |
DNAH1 | ENST00000486752.5 | n.11951C>T | non_coding_transcript_exon_variant | 71/77 | 2 | ||||
DNAH1 | ENST00000488988.5 | n.3280C>T | non_coding_transcript_exon_variant | 19/25 | 2 | ||||
DNAH1 | ENST00000490713.5 | c.2194C>T | p.Arg732Cys | missense_variant, NMD_transcript_variant | 15/20 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00332 AC: 505AN: 152092Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00393 AC: 978AN: 249098Hom.: 7 AF XY: 0.00383 AC XY: 517AN XY: 135144
GnomAD4 exome AF: 0.00348 AC: 5079AN: 1461510Hom.: 18 Cov.: 34 AF XY: 0.00341 AC XY: 2480AN XY: 727018
GnomAD4 genome AF: 0.00331 AC: 504AN: 152210Hom.: 3 Cov.: 32 AF XY: 0.00414 AC XY: 308AN XY: 74414
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at