Variant rs17729253 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_173628.4(DNAH17):c.3834A>G(p.Leu1278=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 1,613,036 control chromosomes in the GnomAD database, including 47,292 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.19 ( 3595 hom., cov: 33)

Exomes 𝑓: 0.24 ( 43697 hom. )

Consequence

DNAH17
NM_173628.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.627

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:

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=-0.57).

BP6

Variant 17-78525039-T-C is Benign according to our data. Variant chr17-78525039-T-C is described in ClinVar as [Benign]. Clinvar id is 402692.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.627 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH17	NM_173628.4 linkuse as main transcript	c.3834A>G	p.Leu1278=	synonymous_variant	25/81	ENST00000389840.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH17	ENST00000389840.7 linkuse as main transcript	c.3834A>G	p.Leu1278=	synonymous_variant	25/81	5	NM_173628.4	P1	Q9UFH2-1

Frequencies

GnomAD3 genomes

AF:

0.193

AC:

29353

AN:

152106

Hom.:

3594

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0636

Gnomad AMI

AF:

0.357

Gnomad AMR

AF:

0.217

Gnomad ASJ

AF:

0.300

Gnomad EAS

AF:

0.0782

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.263

Gnomad OTH

AF:

0.233

GnomAD3 exomes

AF:

0.222

AC:

55319

AN:

248668

Hom.:

6768

AF XY:

0.229

AC XY:

30906

AN XY:

134950

show subpopulations

Gnomad AFR exome

AF:

0.0568

Gnomad AMR exome

AF:

0.206

Gnomad ASJ exome

AF:

0.310

Gnomad EAS exome

AF:

0.0822

Gnomad SAS exome

AF:

0.230

Gnomad FIN exome

AF:

0.195

Gnomad NFE exome

AF:

0.266

Gnomad OTH exome

AF:

0.253

GnomAD4 exome

AF:

0.239

AC:

349636

AN:

1460812

Hom.:

43697

Cov.:

AF XY:

0.241

AC XY:

174839

AN XY:

726612

show subpopulations

Gnomad4 AFR exome

AF:

0.0553

Gnomad4 AMR exome

AF:

0.211

Gnomad4 ASJ exome

AF:

0.311

Gnomad4 EAS exome

AF:

0.0710

Gnomad4 SAS exome

AF:

0.232

Gnomad4 FIN exome

AF:

0.199

Gnomad4 NFE exome

AF:

0.253

Gnomad4 OTH exome

AF:

0.232

GnomAD4 genome

AF:

0.193

AC:

29353

AN:

152224

Hom.:

3595

Cov.:

AF XY:

0.190

AC XY:

14129

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.0637

Gnomad4 AMR

AF:

0.217

Gnomad4 ASJ

AF:

0.300

Gnomad4 EAS

AF:

0.0782

Gnomad4 SAS

AF:

0.218

Gnomad4 FIN

AF:

0.198

Gnomad4 NFE

AF:

0.263

Gnomad4 OTH

AF:

0.230

Alfa

AF:

0.235

Hom.:

3272

Bravo

AF:

0.188

Asia WGS

AF:

0.129

AC:

451

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

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 29, 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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

9.6

DANN

Benign

0.76

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