Variant chr5-13735783-T-C 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_001369.3(DNAH5):c.11570+35A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 1,466,164 control chromosomes in the GnomAD database, including 248,813 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.57 ( 24929 hom., cov: 33)

Exomes 𝑓: 0.58 ( 223884 hom. )

Consequence

DNAH5
NM_001369.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -6.08

Variant links:

Genes affected

DNAH5 (HGNC:2950): (dynein axonemal heavy chain 5) This gene encodes a dynein protein, which is part of a microtubule-associated motor protein complex consisting of heavy, light, and intermediate chains. This protein is an axonemal heavy chain dynein. It functions as a force-generating protein with ATPase activity, whereby the release of ADP is thought to produce the force-producing power stroke. Mutations in this gene cause primary ciliary dyskinesia type 3, as well as Kartagener syndrome, which are both diseases due to ciliary defects. [provided by RefSeq, Oct 2009]

DNAH5 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=-1.04).

BP6

Variant 5-13735783-T-C is Benign according to our data. Variant chr5-13735783-T-C is described in ClinVar as [Benign]. Clinvar id is 257980.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH5	NM_001369.3 linkuse as main transcript	c.11570+35A>G		intron_variant		ENST00000265104.5	NP_001360.1	Q8TE73

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH5	ENST00000265104.5 linkuse as main transcript	c.11570+35A>G		intron_variant		1	NM_001369.3	ENSP00000265104.4		Q8TE73
DNAH5	ENST00000681290.1 linkuse as main transcript	c.11525+35A>G		intron_variant				ENSP00000505288.1		A0A7P0Z455

Frequencies

GnomAD3 genomes

AF:

0.571

AC:

86783

AN:

151984

Hom.:

24916

Cov.:

show subpopulations

Gnomad AFR

AF:

0.526

Gnomad AMI

AF:

0.560

Gnomad AMR

AF:

0.565

Gnomad ASJ

AF:

0.577

Gnomad EAS

AF:

0.573

Gnomad SAS

AF:

0.544

Gnomad FIN

AF:

0.664

Gnomad MID

AF:

0.567

Gnomad NFE

AF:

0.587

Gnomad OTH

AF:

0.571

GnomAD3 exomes

AF:

0.574

AC:

143834

AN:

250574

Hom.:

41599

AF XY:

0.574

AC XY:

77724

AN XY:

135472

show subpopulations

Gnomad AFR exome

AF:

0.526

Gnomad AMR exome

AF:

0.532

Gnomad ASJ exome

AF:

0.572

Gnomad EAS exome

AF:

0.590

Gnomad SAS exome

AF:

0.543

Gnomad FIN exome

AF:

0.654

Gnomad NFE exome

AF:

0.584

Gnomad OTH exome

AF:

0.576

GnomAD4 exome

AF:

0.582

AC:

764659

AN:

1314062

Hom.:

223884

Cov.:

AF XY:

0.581

AC XY:

385102

AN XY:

662578

show subpopulations

Gnomad4 AFR exome

AF:

0.530

Gnomad4 AMR exome

AF:

0.539

Gnomad4 ASJ exome

AF:

0.582

Gnomad4 EAS exome

AF:

0.582

Gnomad4 SAS exome

AF:

0.542

Gnomad4 FIN exome

AF:

0.650

Gnomad4 NFE exome

AF:

0.586

Gnomad4 OTH exome

AF:

0.576

GnomAD4 genome

AF:

0.571

AC:

86846

AN:

152102

Hom.:

24929

Cov.:

AF XY:

0.575

AC XY:

42754

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.526

Gnomad4 AMR

AF:

0.564

Gnomad4 ASJ

AF:

0.577

Gnomad4 EAS

AF:

0.573

Gnomad4 SAS

AF:

0.544

Gnomad4 FIN

AF:

0.664

Gnomad4 NFE

AF:

0.587

Gnomad4 OTH

AF:

0.571

Alfa

AF:

0.577

Hom.:

45316

Bravo

AF:

0.561

Asia WGS

AF:

0.543

AC:

1888

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	Apr 04, 2019	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Primary ciliary dyskinesia 3

Benign:1

Benign, criteria provided, single submitter

clinical testing

Pars Genome Lab

Jun 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.0010

DANN

Benign

0.40

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