Genetic Variant DNAH5:c.4797-29C>A (chr5-13859634-G-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001369.3(DNAH5):c.4797-29C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 1,608,722 control chromosomes in the GnomAD database, including 128,856 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 10532 hom., cov: 32)

Exomes 𝑓: 0.40 ( 118324 hom. )

Consequence

DNAH5
NM_001369.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.160

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=-0.83).

BP6

Variant 5-13859634-G-T is Benign according to our data. Variant chr5-13859634-G-T is described in ClinVar as [Benign]. Clinvar id is 258036.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH5	NM_001369.3 link	c.4797-29C>A		intron_variant	Intron 29 of 78	ENST00000265104.5	NP_001360.1	Q8TE73

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH5	ENST00000265104.5 link	c.4797-29C>A		intron_variant	Intron 29 of 78	1	NM_001369.3	ENSP00000265104.4		Q8TE73
DNAH5	ENST00000681290.1 link	c.4752-29C>A		intron_variant	Intron 29 of 78			ENSP00000505288.1		A0A7P0Z455

Frequencies

GnomAD3 genomes

AF:

0.367

AC:

55777

AN:

151930

Hom.:

10514

Cov.:

show subpopulations

Gnomad AFR

AF:

0.296

Gnomad AMI

AF:

0.311

Gnomad AMR

AF:

0.313

Gnomad ASJ

AF:

0.314

Gnomad EAS

AF:

0.257

Gnomad SAS

AF:

0.445

Gnomad FIN

AF:

0.460

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.414

Gnomad OTH

AF:

0.368

GnomAD3 exomes

AF:

0.376

AC:

94187

AN:

250638

Hom.:

18622

AF XY:

0.384

AC XY:

51950

AN XY:

135456

show subpopulations

Gnomad AFR exome

AF:

0.287

Gnomad AMR exome

AF:

0.275

Gnomad ASJ exome

AF:

0.322

Gnomad EAS exome

AF:

0.237

Gnomad SAS exome

AF:

0.455

Gnomad FIN exome

AF:

0.452

Gnomad NFE exome

AF:

0.411

Gnomad OTH exome

AF:

0.365

GnomAD4 exome

AF:

0.400

AC:

581944

AN:

1456674

Hom.:

118324

Cov.:

AF XY:

0.401

AC XY:

290682

AN XY:

724850

show subpopulations

Gnomad4 AFR exome

AF:

0.300

Gnomad4 AMR exome

AF:

0.282

Gnomad4 ASJ exome

AF:

0.321

Gnomad4 EAS exome

AF:

0.258

Gnomad4 SAS exome

AF:

0.450

Gnomad4 FIN exome

AF:

0.451

Gnomad4 NFE exome

AF:

0.409

Gnomad4 OTH exome

AF:

0.383

GnomAD4 genome

AF:

0.367

AC:

55838

AN:

152048

Hom.:

10532

Cov.:

AF XY:

0.367

AC XY:

27238

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.296

Gnomad4 AMR

AF:

0.313

Gnomad4 ASJ

AF:

0.314

Gnomad4 EAS

AF:

0.259

Gnomad4 SAS

AF:

0.447

Gnomad4 FIN

AF:

0.460

Gnomad4 NFE

AF:

0.414

Gnomad4 OTH

AF:

0.372

Alfa

AF:

0.332

Hom.:

1510

Bravo

AF:

0.348

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Apr 20, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Primary ciliary dyskinesia 3

Benign:1

Jun 15, 2021

Pars Genome Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.38

DANN

Benign

0.51

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