Variant rs11868065 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.3087G>A(p.Pro1029Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 1,609,368 control chromosomes in the GnomAD database, including 217,936 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.51 ( 19943 hom., cov: 31)

Exomes 𝑓: 0.52 ( 197993 hom. )

Consequence

DNAH17
NM_173628.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -6.21

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=-0.8).

BP6

Variant 17-78532509-C-T is Benign according to our data. Variant chr17-78532509-C-T is described in ClinVar as [Benign]. Clinvar id is 402696.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-6.2 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 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.3087G>A	p.Pro1029Pro	synonymous_variant	20/81	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.3087G>A	p.Pro1029Pro	synonymous_variant	20/81	5	NM_173628.4	ENSP00000374490.6		Q9UFH2-1

Frequencies

GnomAD3 genomes

AF:

0.509

AC:

77319

AN:

151862

Hom.:

19934

Cov.:

show subpopulations

Gnomad AFR

AF:

0.489

Gnomad AMI

AF:

0.752

Gnomad AMR

AF:

0.438

Gnomad ASJ

AF:

0.517

Gnomad EAS

AF:

0.429

Gnomad SAS

AF:

0.437

Gnomad FIN

AF:

0.524

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.542

Gnomad OTH

AF:

0.521

GnomAD3 exomes

AF:

0.492

AC:

119418

AN:

242860

Hom.:

29828

AF XY:

0.497

AC XY:

65527

AN XY:

131888

show subpopulations

Gnomad AFR exome

AF:

0.481

Gnomad AMR exome

AF:

0.379

Gnomad ASJ exome

AF:

0.531

Gnomad EAS exome

AF:

0.430

Gnomad SAS exome

AF:

0.441

Gnomad FIN exome

AF:

0.519

Gnomad NFE exome

AF:

0.542

Gnomad OTH exome

AF:

0.517

GnomAD4 exome

AF:

0.520

AC:

757622

AN:

1457388

Hom.:

197993

Cov.:

AF XY:

0.519

AC XY:

375851

AN XY:

724668

show subpopulations

Gnomad4 AFR exome

AF:

0.483

Gnomad4 AMR exome

AF:

0.386

Gnomad4 ASJ exome

AF:

0.530

Gnomad4 EAS exome

AF:

0.440

Gnomad4 SAS exome

AF:

0.447

Gnomad4 FIN exome

AF:

0.524

Gnomad4 NFE exome

AF:

0.534

Gnomad4 OTH exome

AF:

0.518

GnomAD4 genome

AF:

0.509

AC:

77360

AN:

151980

Hom.:

19943

Cov.:

AF XY:

0.505

AC XY:

37499

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.489

Gnomad4 AMR

AF:

0.437

Gnomad4 ASJ

AF:

0.517

Gnomad4 EAS

AF:

0.430

Gnomad4 SAS

AF:

0.437

Gnomad4 FIN

AF:

0.524

Gnomad4 NFE

AF:

0.542

Gnomad4 OTH

AF:

0.518

Alfa

AF:

0.530

Hom.:

10792

Bravo

AF:

0.501

Asia WGS

AF:

0.431

AC:

1499

AN:

3478

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

-0.80

CADD

Benign

0.063

DANN

Benign

0.74

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