Variant 5-13817716-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.6842-22A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0436 in 1,612,932 control chromosomes in the GnomAD database, including 1,827 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.033 ( 109 hom., cov: 33)

Exomes 𝑓: 0.045 ( 1718 hom. )

Consequence

DNAH5
NM_001369.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.16

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:

DNAH5 (HGNC:):

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=-0.79).

BP6

Variant 5-13817716-T-C is Benign according to our data. Variant chr5-13817716-T-C is described in ClinVar as [Benign]. Clinvar id is 258055.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-13817716-T-C is described in Lovd as [Benign].

BA1

GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0517 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.6842-22A>G		intron_variant		ENST00000265104.5	NP_001360.1	Q8TE73

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
DNAH5	ENST00000265104.5 linkuse as main transcript	c.6842-22A>G	intron_variant	1	NM_001369.3	ENSP00000265104.4	Q8TE73
DNAH5	ENST00000681290.1 linkuse as main transcript	c.6797-22A>G	intron_variant			ENSP00000505288.1	A0A7P0Z455
DNAH5	ENST00000683090.1 linkuse as main transcript	n.1773-22A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.0335

AC:

5100

AN:

152146

Hom.:

109

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00864

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0260

Gnomad ASJ

AF:

0.0608

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.0454

Gnomad FIN

AF:

0.0515

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0484

Gnomad OTH

AF:

0.0273

GnomAD3 exomes

AF:

0.0403

AC:

10118

AN:

251196

Hom.:

285

AF XY:

0.0422

AC XY:

5729

AN XY:

135786

show subpopulations

Gnomad AFR exome

AF:

0.00683

Gnomad AMR exome

AF:

0.0172

Gnomad ASJ exome

AF:

0.0564

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.0524

Gnomad FIN exome

AF:

0.0613

Gnomad NFE exome

AF:

0.0495

Gnomad OTH exome

AF:

0.0474

GnomAD4 exome

AF:

0.0446

AC:

65192

AN:

1460668

Hom.:

1718

Cov.:

AF XY:

0.0453

AC XY:

32938

AN XY:

726686

show subpopulations

Gnomad4 AFR exome

AF:

0.00651

Gnomad4 AMR exome

AF:

0.0178

Gnomad4 ASJ exome

AF:

0.0534

Gnomad4 EAS exome

AF:

0.000151

Gnomad4 SAS exome

AF:

0.0530

Gnomad4 FIN exome

AF:

0.0618

Gnomad4 NFE exome

AF:

0.0467

Gnomad4 OTH exome

AF:

0.0457

GnomAD4 genome

AF:

0.0335

AC:

5095

AN:

152264

Hom.:

109

Cov.:

AF XY:

0.0341

AC XY:

2535

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.00861

Gnomad4 AMR

AF:

0.0259

Gnomad4 ASJ

AF:

0.0608

Gnomad4 EAS

AF:

0.000965

Gnomad4 SAS

AF:

0.0450

Gnomad4 FIN

AF:

0.0515

Gnomad4 NFE

AF:

0.0484

Gnomad4 OTH

AF:

0.0265

Alfa

AF:

0.0467

Hom.:

106

Bravo

AF:

0.0291

Asia WGS

AF:

0.0170

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

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	Dec 18, 2019	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

DANN

Benign

0.64

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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