Variant rs13156044 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.4053+32C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 1,559,750 control chromosomes in the GnomAD database, including 11,943 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1162 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10781 hom. )

Consequence

DNAH5
NM_001369.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.890

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:

(HGNC:):

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=-0.9).

BP6

Variant 5-13867742-G-A is Benign according to our data. Variant chr5-13867742-G-A is described in ClinVar as [Benign]. Clinvar id is 258027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-13867742-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 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.4053+32C>T		intron_variant		ENST00000265104.5	NP_001360.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
DNAH5	ENST00000265104.5 linkuse as main transcript	c.4053+32C>T	intron_variant	1	NM_001369.3	ENSP00000265104	P4
	ENST00000503244.2 linkuse as main transcript	n.253+7187G>A	intron_variant, non_coding_transcript_variant	4
DNAH5	ENST00000681290.1 linkuse as main transcript	c.4008+32C>T	intron_variant			ENSP00000505288	A1
	ENST00000637153.1 linkuse as main transcript	n.213+7227G>A	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18369

AN:

151944

Hom.:

1160

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.0559

Gnomad AMR

AF:

0.0755

Gnomad ASJ

AF:

0.0703

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.0469

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.131

Gnomad OTH

AF:

0.109

GnomAD3 exomes

AF:

0.107

AC:

26599

AN:

249558

Hom.:

1604

AF XY:

0.105

AC XY:

14179

AN XY:

134924

show subpopulations

Gnomad AFR exome

AF:

0.120

Gnomad AMR exome

AF:

0.0495

Gnomad ASJ exome

AF:

0.0737

Gnomad EAS exome

AF:

0.0990

Gnomad SAS exome

AF:

0.0490

Gnomad FIN exome

AF:

0.167

Gnomad NFE exome

AF:

0.130

Gnomad OTH exome

AF:

0.111

GnomAD4 exome

AF:

0.120

AC:

169031

AN:

1407686

Hom.:

10781

Cov.:

AF XY:

0.118

AC XY:

82873

AN XY:

703590

show subpopulations

Gnomad4 AFR exome

AF:

0.126

Gnomad4 AMR exome

AF:

0.0543

Gnomad4 ASJ exome

AF:

0.0732

Gnomad4 EAS exome

AF:

0.0915

Gnomad4 SAS exome

AF:

0.0496

Gnomad4 FIN exome

AF:

0.168

Gnomad4 NFE exome

AF:

0.128

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.121

AC:

18381

AN:

152064

Hom.:

1162

Cov.:

AF XY:

0.119

AC XY:

8819

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.125

Gnomad4 AMR

AF:

0.0754

Gnomad4 ASJ

AF:

0.0703

Gnomad4 EAS

AF:

0.104

Gnomad4 SAS

AF:

0.0474

Gnomad4 FIN

AF:

0.174

Gnomad4 NFE

AF:

0.131

Gnomad4 OTH

AF:

0.108

Alfa

AF:

0.119

Hom.:

1341

Bravo

AF:

0.113

Asia WGS

AF:

0.0880

AC:

306

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	clinical testing	GeneDx	Nov 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

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

-0.90

CADD

Benign

0.053

DANN

Benign

0.71

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