Variant 17-78560729-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_173628.4(DNAH17):c.2031+11G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 1,544,228 control chromosomes in the GnomAD database, including 113,787 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.33 ( 8737 hom., cov: 31)

Exomes 𝑓: 0.38 ( 105050 hom. )

Consequence

DNAH17
NM_173628.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.497

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 17-78560729-C-T is Benign according to our data. Variant chr17-78560729-C-T is described in ClinVar as [Benign]. Clinvar id is 402700.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 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.2031+11G>A		intron_variant		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.2031+11G>A		intron_variant		5	NM_173628.4	ENSP00000374490.6		Q9UFH2-1
DNAH17	ENST00000589793.1 linkuse as main transcript	n.1243+11G>A		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.328

AC:

49835

AN:

151922

Hom.:

8733

Cov.:

show subpopulations

Gnomad AFR

AF:

0.237

Gnomad AMI

AF:

0.557

Gnomad AMR

AF:

0.256

Gnomad ASJ

AF:

0.329

Gnomad EAS

AF:

0.387

Gnomad SAS

AF:

0.537

Gnomad FIN

AF:

0.312

Gnomad MID

AF:

0.357

Gnomad NFE

AF:

0.380

Gnomad OTH

AF:

0.321

GnomAD3 exomes

AF:

0.356

AC:

54398

AN:

153016

Hom.:

10543

AF XY:

0.372

AC XY:

29909

AN XY:

80444

show subpopulations

Gnomad AFR exome

AF:

0.242

Gnomad AMR exome

AF:

0.215

Gnomad ASJ exome

AF:

0.330

Gnomad EAS exome

AF:

0.374

Gnomad SAS exome

AF:

0.541

Gnomad FIN exome

AF:

0.307

Gnomad NFE exome

AF:

0.376

Gnomad OTH exome

AF:

0.339

GnomAD4 exome

AF:

0.383

AC:

533788

AN:

1392188

Hom.:

105050

Cov.:

AF XY:

0.388

AC XY:

265686

AN XY:

685482

show subpopulations

Gnomad4 AFR exome

AF:

0.238

Gnomad4 AMR exome

AF:

0.217

Gnomad4 ASJ exome

AF:

0.327

Gnomad4 EAS exome

AF:

0.419

Gnomad4 SAS exome

AF:

0.543

Gnomad4 FIN exome

AF:

0.315

Gnomad4 NFE exome

AF:

0.385

Gnomad4 OTH exome

AF:

0.374

GnomAD4 genome

AF:

0.328

AC:

49839

AN:

152040

Hom.:

8737

Cov.:

AF XY:

0.329

AC XY:

24411

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.237

Gnomad4 AMR

AF:

0.255

Gnomad4 ASJ

AF:

0.329

Gnomad4 EAS

AF:

0.387

Gnomad4 SAS

AF:

0.538

Gnomad4 FIN

AF:

0.312

Gnomad4 NFE

AF:

0.380

Gnomad4 OTH

AF:

0.318

Alfa

AF:

0.265

Hom.:

1016

Bravo

AF:

0.314

Asia WGS

AF:

0.468

AC:

1627

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

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 -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.53

DANN

Benign

0.75

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