Genetic Variant DNAH17:p.Thr2474Thr (chr17-78485611-C-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_173628.4(DNAH17):c.7422G>C(p.Thr2474Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 1,613,232 control chromosomes in the GnomAD database, including 356,357 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.65 ( 32175 hom., cov: 31)

Exomes 𝑓: 0.67 ( 324182 hom. )

Consequence

DNAH17
NM_173628.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -4.15

Variant links:

Genes affected

DNAH17 (HGNC:2946): (dynein axonemal heavy chain 17) Dyneins are microtubule-associated motor protein complexes composed of several heavy, light, and intermediate chains. DNAH17 is a heavy chain associated with axonemal dynein (Milisav and Affara, 1998 [PubMed 9545504]).[supplied by OMIM, Mar 2008]

DNAH17 links:

DNAH17-AS1 (HGNC:48594): (DNAH17 antisense RNA 1)

DNAH17-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 17-78485611-C-G is Benign according to our data. Variant chr17-78485611-C-G is described in ClinVar as [Benign]. Clinvar id is 402680.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-4.15 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH17	NM_173628.4 link	c.7422G>C	p.Thr2474Thr	synonymous_variant	Exon 47 of 81	ENST00000389840.7	NP_775899.3	Q9UFH2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH17	ENST00000389840.7 link	c.7422G>C	p.Thr2474Thr	synonymous_variant	Exon 47 of 81	5	NM_173628.4	ENSP00000374490.6		Q9UFH2-1

Frequencies

GnomAD3 genomes

AF:

0.647

AC:

98306

AN:

151872

Hom.:

32155

Cov.:

show subpopulations

Gnomad AFR

AF:

0.574

Gnomad AMI

AF:

0.671

Gnomad AMR

AF:

0.723

Gnomad ASJ

AF:

0.687

Gnomad EAS

AF:

0.587

Gnomad SAS

AF:

0.691

Gnomad FIN

AF:

0.678

Gnomad MID

AF:

0.652

Gnomad NFE

AF:

0.668

Gnomad OTH

AF:

0.667

GnomAD3 exomes

AF:

0.676

AC:

167640

AN:

248154

Hom.:

57023

AF XY:

0.675

AC XY:

90937

AN XY:

134650

show subpopulations

Gnomad AFR exome

AF:

0.572

Gnomad AMR exome

AF:

0.762

Gnomad ASJ exome

AF:

0.677

Gnomad EAS exome

AF:

0.582

Gnomad SAS exome

AF:

0.705

Gnomad FIN exome

AF:

0.671

Gnomad NFE exome

AF:

0.671

Gnomad OTH exome

AF:

0.677

GnomAD4 exome

AF:

0.665

AC:

971862

AN:

1461242

Hom.:

324182

Cov.:

AF XY:

0.666

AC XY:

483780

AN XY:

726886

show subpopulations

Gnomad4 AFR exome

AF:

0.570

Gnomad4 AMR exome

AF:

0.754

Gnomad4 ASJ exome

AF:

0.673

Gnomad4 EAS exome

AF:

0.574

Gnomad4 SAS exome

AF:

0.703

Gnomad4 FIN exome

AF:

0.671

Gnomad4 NFE exome

AF:

0.665

Gnomad4 OTH exome

AF:

0.659

GnomAD4 genome

AF:

0.647

AC:

98375

AN:

151990

Hom.:

32175

Cov.:

AF XY:

0.649

AC XY:

48252

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.574

Gnomad4 AMR

AF:

0.723

Gnomad4 ASJ

AF:

0.687

Gnomad4 EAS

AF:

0.587

Gnomad4 SAS

AF:

0.691

Gnomad4 FIN

AF:

0.678

Gnomad4 NFE

AF:

0.668

Gnomad4 OTH

AF:

0.670

Alfa

AF:

0.642

Hom.:

8315

Bravo

AF:

0.647

EpiCase

AF:

0.678

EpiControl

AF:

0.679

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

May 04, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Oct 17, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.012

DANN

Benign

0.67

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over