Variant 17-78427070-C-T 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.12627G>A(p.Pro4209Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0908 in 1,591,330 control chromosomes in the GnomAD database, including 7,002 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.087 ( 623 hom., cov: 32)

Exomes 𝑓: 0.091 ( 6379 hom. )

Consequence

DNAH17
NM_173628.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.51

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=-0.65).

BP6

Variant 17-78427070-C-T is Benign according to our data. Variant chr17-78427070-C-T is described in ClinVar as [Benign]. Clinvar id is 402673.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.51 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.102 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.12627G>A	p.Pro4209Pro	synonymous_variant	78/81	ENST00000389840.7	NP_775899.3	Q9UFH2-1
DNAH17	XM_011525416.3 linkuse as main transcript	c.12639G>A	p.Pro4213Pro	synonymous_variant	78/81		XP_011523718.1
DNAH17	XM_024451013.2 linkuse as main transcript	c.12495G>A	p.Pro4165Pro	synonymous_variant	77/80		XP_024306781.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH17	ENST00000389840.7 linkuse as main transcript	c.12627G>A	p.Pro4209Pro	synonymous_variant	78/81	5	NM_173628.4	ENSP00000374490.6		Q9UFH2-1

Frequencies

GnomAD3 genomes

AF:

0.0872

AC:

13257

AN:

152094

Hom.:

622

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0936

Gnomad AMI

AF:

0.0362

Gnomad AMR

AF:

0.0691

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.0313

Gnomad SAS

AF:

0.110

Gnomad FIN

AF:

0.0424

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.0960

Gnomad OTH

AF:

0.0919

GnomAD3 exomes

AF:

0.0822

AC:

17452

AN:

212394

Hom.:

832

AF XY:

0.0853

AC XY:

9746

AN XY:

114222

show subpopulations

Gnomad AFR exome

AF:

0.0890

Gnomad AMR exome

AF:

0.0509

Gnomad ASJ exome

AF:

0.117

Gnomad EAS exome

AF:

0.0317

Gnomad SAS exome

AF:

0.115

Gnomad FIN exome

AF:

0.0474

Gnomad NFE exome

AF:

0.0931

Gnomad OTH exome

AF:

0.104

GnomAD4 exome

AF:

0.0912

AC:

131261

AN:

1439118

Hom.:

6379

Cov.:

AF XY:

0.0926

AC XY:

66122

AN XY:

713684

show subpopulations

Gnomad4 AFR exome

AF:

0.0947

Gnomad4 AMR exome

AF:

0.0535

Gnomad4 ASJ exome

AF:

0.112

Gnomad4 EAS exome

AF:

0.0282

Gnomad4 SAS exome

AF:

0.113

Gnomad4 FIN exome

AF:

0.0483

Gnomad4 NFE exome

AF:

0.0941

Gnomad4 OTH exome

AF:

0.0940

GnomAD4 genome

AF:

0.0871

AC:

13263

AN:

152212

Hom.:

623

Cov.:

AF XY:

0.0850

AC XY:

6322

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.0935

Gnomad4 AMR

AF:

0.0691

Gnomad4 ASJ

AF:

0.110

Gnomad4 EAS

AF:

0.0314

Gnomad4 SAS

AF:

0.110

Gnomad4 FIN

AF:

0.0424

Gnomad4 NFE

AF:

0.0960

Gnomad4 OTH

AF:

0.0914

Alfa

AF:

0.0939

Hom.:

372

Bravo

AF:

0.0869

Asia WGS

AF:

0.0790

AC:

279

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 21, 2018	- -

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

Nov 20, 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

-0.65

CADD

Benign

2.9

DANN

Benign

0.90

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