Variant chr17-78425383-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.13104G>A(p.Pro4368=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,613,606 control chromosomes in the GnomAD database, including 23,049 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2446 hom., cov: 32)

Exomes 𝑓: 0.16 ( 20603 hom. )

Consequence

DNAH17
NM_173628.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.942

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=-0.79).

BP6

Variant 17-78425383-C-T is Benign according to our data. Variant chr17-78425383-C-T is described in ClinVar as [Benign]. Clinvar id is 402670.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.942 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
DNAH17	NM_173628.4 linkuse as main transcript	c.13104G>A	p.Pro4368=	synonymous_variant	80/81	ENST00000389840.7	NP_775899.3
DNAH17	XM_011525416.3 linkuse as main transcript	c.13116G>A	p.Pro4372=	synonymous_variant	80/81		XP_011523718.1
DNAH17	XM_024451013.2 linkuse as main transcript	c.12972G>A	p.Pro4324=	synonymous_variant	79/80		XP_024306781.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH17	ENST00000389840.7 linkuse as main transcript	c.13104G>A	p.Pro4368=	synonymous_variant	80/81	5	NM_173628.4	ENSP00000374490	P1	Q9UFH2-1
DNAH17	ENST00000586052.5 linkuse as main transcript	n.6265G>A		non_coding_transcript_exon_variant	34/35	5
DNAH17	ENST00000590227.5 linkuse as main transcript	n.2778G>A		non_coding_transcript_exon_variant	12/13	2
DNAH17	ENST00000591369.5 linkuse as main transcript	c.*35G>A		3_prime_UTR_variant, NMD_transcript_variant	27/28	5		ENSP00000466150

Frequencies

GnomAD3 genomes

AF:

0.173

AC:

26288

AN:

151974

Hom.:

2443

Cov.:

show subpopulations

Gnomad AFR

AF:

0.230

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.231

Gnomad EAS

AF:

0.0306

Gnomad SAS

AF:

0.152

Gnomad FIN

AF:

0.112

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.167

Gnomad OTH

AF:

0.179

GnomAD3 exomes

AF:

0.150

AC:

37695

AN:

251026

Hom.:

3169

AF XY:

0.154

AC XY:

20877

AN XY:

135662

show subpopulations

Gnomad AFR exome

AF:

0.234

Gnomad AMR exome

AF:

0.0905

Gnomad ASJ exome

AF:

0.227

Gnomad EAS exome

AF:

0.0352

Gnomad SAS exome

AF:

0.162

Gnomad FIN exome

AF:

0.114

Gnomad NFE exome

AF:

0.171

Gnomad OTH exome

AF:

0.166

GnomAD4 exome

AF:

0.163

AC:

238682

AN:

1461514

Hom.:

20603

Cov.:

AF XY:

0.163

AC XY:

118595

AN XY:

727036

show subpopulations

Gnomad4 AFR exome

AF:

0.235

Gnomad4 AMR exome

AF:

0.0931

Gnomad4 ASJ exome

AF:

0.233

Gnomad4 EAS exome

AF:

0.0217

Gnomad4 SAS exome

AF:

0.163

Gnomad4 FIN exome

AF:

0.113

Gnomad4 NFE exome

AF:

0.170

Gnomad4 OTH exome

AF:

0.163

GnomAD4 genome

AF:

0.173

AC:

26308

AN:

152092

Hom.:

2446

Cov.:

AF XY:

0.168

AC XY:

12512

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.230

Gnomad4 AMR

AF:

0.130

Gnomad4 ASJ

AF:

0.231

Gnomad4 EAS

AF:

0.0305

Gnomad4 SAS

AF:

0.152

Gnomad4 FIN

AF:

0.112

Gnomad4 NFE

AF:

0.167

Gnomad4 OTH

AF:

0.177

Alfa

AF:

0.180

Hom.:

1114

Bravo

AF:

0.178

Asia WGS

AF:

0.0790

AC:

274

AN:

3478

EpiCase

AF:

0.168

EpiControl

AF:

0.176

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

Nov 18, 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

-0.79

CADD

Benign

0.88

DANN

Benign

0.92

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