Variant 17-78466688-G-A 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.8907C>T(p.Ser2969Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 1,611,012 control chromosomes in the GnomAD database, including 468,641 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.67 ( 36293 hom., cov: 31)

Exomes 𝑓: 0.77 ( 432348 hom. )

Consequence

DNAH17
NM_173628.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.209

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 (HGNC:):

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=-0.82).

BP6

Variant 17-78466688-G-A is Benign according to our data. Variant chr17-78466688-G-A is described in ClinVar as [Benign]. Clinvar id is 402677.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.209 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 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.8907C>T	p.Ser2969Ser	synonymous_variant	56/81	ENST00000389840.7	NP_775899.3	Q9UFH2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
DNAH17	ENST00000389840.7 linkuse as main transcript	c.8907C>T	p.Ser2969Ser	synonymous_variant	56/81	5	NM_173628.4	ENSP00000374490.6	Q9UFH2-1
DNAH17	ENST00000586052.5 linkuse as main transcript	n.2289C>T		non_coding_transcript_exon_variant	12/35	5
DNAH17	ENST00000591369.5 linkuse as main transcript	n.507C>T		non_coding_transcript_exon_variant	3/28	5		ENSP00000466150.1	K7ELN3

Frequencies

GnomAD3 genomes

AF:

0.670

AC:

101790

AN:

151894

Hom.:

36283

Cov.:

show subpopulations

Gnomad AFR

AF:

0.404

Gnomad AMI

AF:

0.700

Gnomad AMR

AF:

0.762

Gnomad ASJ

AF:

0.764

Gnomad EAS

AF:

0.830

Gnomad SAS

AF:

0.623

Gnomad FIN

AF:

0.752

Gnomad MID

AF:

0.729

Gnomad NFE

AF:

0.783

Gnomad OTH

AF:

0.708

GnomAD3 exomes

AF:

0.738

AC:

181658

AN:

246148

Hom.:

68407

AF XY:

0.737

AC XY:

98620

AN XY:

133798

show subpopulations

Gnomad AFR exome

AF:

0.387

Gnomad AMR exome

AF:

0.779

Gnomad ASJ exome

AF:

0.765

Gnomad EAS exome

AF:

0.822

Gnomad SAS exome

AF:

0.628

Gnomad FIN exome

AF:

0.757

Gnomad NFE exome

AF:

0.782

Gnomad OTH exome

AF:

0.773

GnomAD4 exome

AF:

0.766

AC:

1117628

AN:

1459000

Hom.:

432348

Cov.:

AF XY:

0.763

AC XY:

553377

AN XY:

725678

show subpopulations

Gnomad4 AFR exome

AF:

0.392

Gnomad4 AMR exome

AF:

0.778

Gnomad4 ASJ exome

AF:

0.765

Gnomad4 EAS exome

AF:

0.819

Gnomad4 SAS exome

AF:

0.626

Gnomad4 FIN exome

AF:

0.754

Gnomad4 NFE exome

AF:

0.787

Gnomad4 OTH exome

AF:

0.754

GnomAD4 genome

AF:

0.670

AC:

101822

AN:

152012

Hom.:

36293

Cov.:

AF XY:

0.670

AC XY:

49750

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.404

Gnomad4 AMR

AF:

0.762

Gnomad4 ASJ

AF:

0.764

Gnomad4 EAS

AF:

0.830

Gnomad4 SAS

AF:

0.622

Gnomad4 FIN

AF:

0.752

Gnomad4 NFE

AF:

0.783

Gnomad4 OTH

AF:

0.710

Alfa

AF:

0.731

Hom.:

22857

Bravo

AF:

0.661

Asia WGS

AF:

0.705

AC:

2448

AN:

3478

EpiCase

AF:

0.780

EpiControl

AF:

0.779

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

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

-0.82

CADD

Benign

0.037

DANN

Benign

0.34

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