Variant 17-78485526-A-G 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.7483+24T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 1,551,840 control chromosomes in the GnomAD database, including 425,860 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.78 ( 46183 hom., cov: 31)

Exomes 𝑓: 0.74 ( 379677 hom. )

Consequence

DNAH17
NM_173628.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.01

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=-0.91).

BP6

Variant 17-78485526-A-G is Benign according to our data. Variant chr17-78485526-A-G is described in ClinVar as [Benign]. Clinvar id is 1269897.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 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.7483+24T>C		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.7483+24T>C		intron_variant		5	NM_173628.4	ENSP00000374490.6		Q9UFH2-1

Frequencies

GnomAD3 genomes

AF:

0.777

AC:

117996

AN:

151934

Hom.:

46136

Cov.:

show subpopulations

Gnomad AFR

AF:

0.856

Gnomad AMI

AF:

0.740

Gnomad AMR

AF:

0.833

Gnomad ASJ

AF:

0.733

Gnomad EAS

AF:

0.696

Gnomad SAS

AF:

0.795

Gnomad FIN

AF:

0.721

Gnomad MID

AF:

0.778

Gnomad NFE

AF:

0.731

Gnomad OTH

AF:

0.786

GnomAD3 exomes

AF:

0.752

AC:

125428

AN:

166872

Hom.:

47592

AF XY:

0.747

AC XY:

67029

AN XY:

89748

show subpopulations

Gnomad AFR exome

AF:

0.854

Gnomad AMR exome

AF:

0.861

Gnomad ASJ exome

AF:

0.713

Gnomad EAS exome

AF:

0.686

Gnomad SAS exome

AF:

0.790

Gnomad FIN exome

AF:

0.698

Gnomad NFE exome

AF:

0.711

Gnomad OTH exome

AF:

0.751

GnomAD4 exome

AF:

0.735

AC:

1029374

AN:

1399788

Hom.:

379677

Cov.:

AF XY:

0.735

AC XY:

508307

AN XY:

691224

show subpopulations

Gnomad4 AFR exome

AF:

0.862

Gnomad4 AMR exome

AF:

0.856

Gnomad4 ASJ exome

AF:

0.718

Gnomad4 EAS exome

AF:

0.696

Gnomad4 SAS exome

AF:

0.797

Gnomad4 FIN exome

AF:

0.711

Gnomad4 NFE exome

AF:

0.725

Gnomad4 OTH exome

AF:

0.741

GnomAD4 genome

AF:

0.777

AC:

118105

AN:

152052

Hom.:

46183

Cov.:

AF XY:

0.777

AC XY:

57722

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.856

Gnomad4 AMR

AF:

0.833

Gnomad4 ASJ

AF:

0.733

Gnomad4 EAS

AF:

0.696

Gnomad4 SAS

AF:

0.795

Gnomad4 FIN

AF:

0.721

Gnomad4 NFE

AF:

0.731

Gnomad4 OTH

AF:

0.787

Alfa

AF:

0.753

Hom.:

7970

Bravo

AF:

0.788

Asia WGS

AF:

0.811

AC:

2822

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

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 11, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.1

DANN

Benign

0.26

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