Variant 5-13914687-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.1198-45A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 1,580,620 control chromosomes in the GnomAD database, including 128,228 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.44 ( 15251 hom., cov: 32)

Exomes 𝑓: 0.39 ( 112977 hom. )

Consequence

DNAH5
NM_001369.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.22

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=-0.82).

BP6

Variant 5-13914687-T-C is Benign according to our data. Variant chr5-13914687-T-C is described in ClinVar as [Benign]. Clinvar id is 257988.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH5	NM_001369.3 linkuse as main transcript	c.1198-45A>G		intron_variant		ENST00000265104.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH5	ENST00000265104.5 linkuse as main transcript	c.1198-45A>G		intron_variant		1	NM_001369.3	P4

Frequencies

GnomAD3 genomes

AF:

0.436

AC:

66257

AN:

151800

Hom.:

15247

Cov.:

show subpopulations

Gnomad AFR

AF:

0.528

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.412

Gnomad ASJ

AF:

0.409

Gnomad EAS

AF:

0.852

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.327

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.379

Gnomad OTH

AF:

0.428

GnomAD3 exomes

AF:

0.420

AC:

104640

AN:

248932

Hom.:

24193

AF XY:

0.414

AC XY:

55729

AN XY:

134718

show subpopulations

Gnomad AFR exome

AF:

0.534

Gnomad AMR exome

AF:

0.391

Gnomad ASJ exome

AF:

0.422

Gnomad EAS exome

AF:

0.861

Gnomad SAS exome

AF:

0.357

Gnomad FIN exome

AF:

0.329

Gnomad NFE exome

AF:

0.376

Gnomad OTH exome

AF:

0.410

GnomAD4 exome

AF:

0.386

AC:

551574

AN:

1428702

Hom.:

112977

Cov.:

AF XY:

0.385

AC XY:

274039

AN XY:

712222

show subpopulations

Gnomad4 AFR exome

AF:

0.530

Gnomad4 AMR exome

AF:

0.395

Gnomad4 ASJ exome

AF:

0.420

Gnomad4 EAS exome

AF:

0.841

Gnomad4 SAS exome

AF:

0.356

Gnomad4 FIN exome

AF:

0.339

Gnomad4 NFE exome

AF:

0.368

Gnomad4 OTH exome

AF:

0.406

GnomAD4 genome

AF:

0.436

AC:

66288

AN:

151918

Hom.:

15251

Cov.:

AF XY:

0.435

AC XY:

32280

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.528

Gnomad4 AMR

AF:

0.412

Gnomad4 ASJ

AF:

0.409

Gnomad4 EAS

AF:

0.851

Gnomad4 SAS

AF:

0.373

Gnomad4 FIN

AF:

0.327

Gnomad4 NFE

AF:

0.379

Gnomad4 OTH

AF:

0.428

Alfa

AF:

0.387

Hom.:

2126

Bravo

AF:

0.450

Asia WGS

AF:

0.573

AC:

1988

AN:

3476

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	Nov 10, 2018	- -

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

-0.82

CADD

Benign

4.1

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