rs61742072
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_173628.4(DNAH17):c.11857C>T(p.His3953Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 1,611,708 control chromosomes in the GnomAD database, including 22,566 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict 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. H3953R) 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.11857C>T | p.His3953Tyr | missense_variant | 74/81 | ENST00000389840.7 | |
DNAH17 | XM_011525416.3 | c.11869C>T | p.His3957Tyr | missense_variant | 74/81 | ||
DNAH17 | XM_024451013.2 | c.11725C>T | p.His3909Tyr | missense_variant | 73/80 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH17 | ENST00000389840.7 | c.11857C>T | p.His3953Tyr | missense_variant | 74/81 | 5 | NM_173628.4 | P1 | |
DNAH17 | ENST00000586052.5 | n.4993C>T | non_coding_transcript_exon_variant | 28/35 | 5 | ||||
DNAH17 | ENST00000590227.5 | n.1531C>T | non_coding_transcript_exon_variant | 6/13 | 2 | ||||
DNAH17 | ENST00000591369.5 | c.3460C>T | p.His1154Tyr | missense_variant, NMD_transcript_variant | 21/28 | 5 |
Frequencies
GnomAD3 genomes AF: 0.128 AC: 19476AN: 152112Hom.: 1505 Cov.: 29
GnomAD3 exomes AF: 0.142 AC: 35251AN: 248778Hom.: 2874 AF XY: 0.149 AC XY: 20134AN XY: 135106
GnomAD4 exome AF: 0.165 AC: 240842AN: 1459478Hom.: 21060 Cov.: 35 AF XY: 0.165 AC XY: 119862AN XY: 725962
GnomAD4 genome AF: 0.128 AC: 19476AN: 152230Hom.: 1506 Cov.: 29 AF XY: 0.125 AC XY: 9282AN XY: 74448
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 | Nov 18, 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 | Apr 19, 2019 | This variant is associated with the following publications: (PMID: 30389748) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at