Variant 17-78500410-A-G 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.5535T>C(p.Pro1845Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 1,610,380 control chromosomes in the GnomAD database, including 563,323 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.87 ( 57830 hom., cov: 32)

Exomes 𝑓: 0.83 ( 505493 hom. )

Consequence

DNAH17
NM_173628.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.27

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:):

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=-0.92).

BP6

Variant 17-78500410-A-G is Benign according to our data. Variant chr17-78500410-A-G is described in ClinVar as [Benign]. Clinvar id is 402685.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.27 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH17	NM_173628.4 linkuse as main transcript	c.5535T>C	p.Pro1845Pro	synonymous_variant	36/81	ENST00000389840.7	NP_775899.3	Q9UFH2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH17	ENST00000389840.7 linkuse as main transcript	c.5535T>C	p.Pro1845Pro	synonymous_variant	36/81	5	NM_173628.4	ENSP00000374490.6		Q9UFH2-1
DNAH17-AS1	ENST00000598378.2 linkuse as main transcript	n.1951A>G		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.868

AC:

132048

AN:

152106

Hom.:

57768

Cov.:

show subpopulations

Gnomad AFR

AF:

0.967

Gnomad AMI

AF:

0.821

Gnomad AMR

AF:

0.877

Gnomad ASJ

AF:

0.849

Gnomad EAS

AF:

0.979

Gnomad SAS

AF:

0.931

Gnomad FIN

AF:

0.809

Gnomad MID

AF:

0.870

Gnomad NFE

AF:

0.804

Gnomad OTH

AF:

0.872

GnomAD3 exomes

AF:

0.862

AC:

209785

AN:

243284

Hom.:

91093

AF XY:

0.860

AC XY:

114070

AN XY:

132710

show subpopulations

Gnomad AFR exome

AF:

0.970

Gnomad AMR exome

AF:

0.916

Gnomad ASJ exome

AF:

0.846

Gnomad EAS exome

AF:

0.977

Gnomad SAS exome

AF:

0.928

Gnomad FIN exome

AF:

0.809

Gnomad NFE exome

AF:

0.807

Gnomad OTH exome

AF:

0.845

GnomAD4 exome

AF:

0.831

AC:

1211882

AN:

1458156

Hom.:

505493

Cov.:

AF XY:

0.832

AC XY:

603747

AN XY:

725336

show subpopulations

Gnomad4 AFR exome

AF:

0.975

Gnomad4 AMR exome

AF:

0.913

Gnomad4 ASJ exome

AF:

0.843

Gnomad4 EAS exome

AF:

0.988

Gnomad4 SAS exome

AF:

0.926

Gnomad4 FIN exome

AF:

0.809

Gnomad4 NFE exome

AF:

0.810

Gnomad4 OTH exome

AF:

0.850

GnomAD4 genome

AF:

0.868

AC:

132169

AN:

152224

Hom.:

57830

Cov.:

AF XY:

0.871

AC XY:

64815

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.967

Gnomad4 AMR

AF:

0.877

Gnomad4 ASJ

AF:

0.849

Gnomad4 EAS

AF:

0.978

Gnomad4 SAS

AF:

0.931

Gnomad4 FIN

AF:

0.809

Gnomad4 NFE

AF:

0.804

Gnomad4 OTH

AF:

0.873

Alfa

AF:

0.831

Hom.:

29337

Bravo

AF:

0.878

Asia WGS

AF:

0.965

AC:

3357

AN:

3478

EpiCase

AF:

0.805

EpiControl

AF:

0.811

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -

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, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 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). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.042

DANN

Benign

0.42

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