Variant rs795527 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 ENST00000265104.5(DNAH5):c.5114+30G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0515 in 1,601,962 control chromosomes in the GnomAD database, including 2,439 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.062 ( 309 hom., cov: 33)

Exomes 𝑓: 0.050 ( 2130 hom. )

Consequence

DNAH5
ENST00000265104.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.05

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=-0.86).

BP6

Variant 5-13850622-C-A is Benign according to our data. Variant chr5-13850622-C-A is described in ClinVar as [Benign]. Clinvar id is 258039.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.077 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.5114+30G>T		intron_variant		ENST00000265104.5	NP_001360.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH5	ENST00000265104.5 linkuse as main transcript	c.5114+30G>T		intron_variant		1	NM_001369.3	ENSP00000265104	P4
DNAH5	ENST00000681290.1 linkuse as main transcript	c.5069+30G>T		intron_variant				ENSP00000505288	A1

Frequencies

GnomAD3 genomes

AF:

0.0617

AC:

9378

AN:

152044

Hom.:

308

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0792

Gnomad AMI

AF:

0.0496

Gnomad AMR

AF:

0.0670

Gnomad ASJ

AF:

0.0447

Gnomad EAS

AF:

0.0339

Gnomad SAS

AF:

0.0289

Gnomad FIN

AF:

0.104

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0492

Gnomad OTH

AF:

0.0511

GnomAD3 exomes

AF:

0.0564

AC:

14140

AN:

250760

Hom.:

485

AF XY:

0.0523

AC XY:

7097

AN XY:

135594

show subpopulations

Gnomad AFR exome

AF:

0.0832

Gnomad AMR exome

AF:

0.0942

Gnomad ASJ exome

AF:

0.0425

Gnomad EAS exome

AF:

0.0326

Gnomad SAS exome

AF:

0.0298

Gnomad FIN exome

AF:

0.0967

Gnomad NFE exome

AF:

0.0462

Gnomad OTH exome

AF:

0.0447

GnomAD4 exome

AF:

0.0504

AC:

73118

AN:

1449800

Hom.:

2130

Cov.:

AF XY:

0.0493

AC XY:

35586

AN XY:

722146

show subpopulations

Gnomad4 AFR exome

AF:

0.0808

Gnomad4 AMR exome

AF:

0.0923

Gnomad4 ASJ exome

AF:

0.0469

Gnomad4 EAS exome

AF:

0.0256

Gnomad4 SAS exome

AF:

0.0321

Gnomad4 FIN exome

AF:

0.0920

Gnomad4 NFE exome

AF:

0.0485

Gnomad4 OTH exome

AF:

0.0477

GnomAD4 genome

AF:

0.0617

AC:

9393

AN:

152162

Hom.:

309

Cov.:

AF XY:

0.0630

AC XY:

4684

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.0793

Gnomad4 AMR

AF:

0.0672

Gnomad4 ASJ

AF:

0.0447

Gnomad4 EAS

AF:

0.0332

Gnomad4 SAS

AF:

0.0293

Gnomad4 FIN

AF:

0.104

Gnomad4 NFE

AF:

0.0492

Gnomad4 OTH

AF:

0.0506

Alfa

AF:

0.0334

Hom.:

Bravo

AF:

0.0598

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	clinical testing	GeneDx	Mar 10, 2019	- -
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

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.0050

DANN

Benign

0.66

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