chr17-78437816-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_173628.4(DNAH17):āc.11858A>Gā(p.His3953Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.991 in 1,612,240 control chromosomes in the GnomAD database, including 792,214 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H3953Y) has been classified as Benign.
Frequency
Consequence
NM_173628.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH17 | NM_173628.4 | c.11858A>G | p.His3953Arg | missense_variant | 74/81 | ENST00000389840.7 | |
DNAH17 | XM_011525416.3 | c.11870A>G | p.His3957Arg | missense_variant | 74/81 | ||
DNAH17 | XM_024451013.2 | c.11726A>G | p.His3909Arg | missense_variant | 73/80 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH17 | ENST00000389840.7 | c.11858A>G | p.His3953Arg | missense_variant | 74/81 | 5 | NM_173628.4 | P1 | |
DNAH17 | ENST00000586052.5 | n.4994A>G | non_coding_transcript_exon_variant | 28/35 | 5 | ||||
DNAH17 | ENST00000590227.5 | n.1532A>G | non_coding_transcript_exon_variant | 6/13 | 2 | ||||
DNAH17 | ENST00000591369.5 | c.3461A>G | p.His1154Arg | missense_variant, NMD_transcript_variant | 21/28 | 5 |
Frequencies
GnomAD3 genomes AF: 0.954 AC: 145230AN: 152158Hom.: 69664 Cov.: 33
GnomAD3 exomes AF: 0.987 AC: 245818AN: 249138Hom.: 121459 AF XY: 0.990 AC XY: 133884AN XY: 135268
GnomAD4 exome AF: 0.995 AC: 1452017AN: 1459964Hom.: 722525 Cov.: 56 AF XY: 0.995 AC XY: 722794AN XY: 726246
GnomAD4 genome AF: 0.954 AC: 145307AN: 152276Hom.: 69689 Cov.: 33 AF XY: 0.956 AC XY: 71138AN XY: 74442
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
DNAH17-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at