NM_001369.3:c.3835-3delT

Variant names:

• chr5-13867994-TA-T
• rs35398031
• NM_001369.3:c.3835-3delT

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_001369.3(DNAH5):​c.3835-3delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.40 (12176 hom., cov: 0)
  • Exomes 𝑓: 0.43 (137623 hom.)
• Consequence: DNAH5 NM_001369.3 splice_region, intron
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:10
• Conservation: PhyloP100: 0.454

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]

ENSG00000251423 (HGNC:40187):

ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

• BP6: Variant 5-13867994-TA-T is Benign according to our data. Variant chr5-13867994-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 215494.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-13867994-TA-T is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH5	NM_001369.3	c.3835-3delT		splice_region_variant, intron_variant	Intron 24 of 78	ENST00000265104.5	NP_001360.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH5	ENST00000265104.5	c.3835-3delT		splice_region_variant, intron_variant	Intron 24 of 78	1	NM_001369.3	ENSP00000265104.4
DNAH5	ENST00000681290.1	c.3790-3delT		splice_region_variant, intron_variant	Intron 24 of 78			ENSP00000505288.1
ENSG00000251423	ENST00000503244.2	n.253+7440delA		intron_variant	Intron 1 of 2	4
ENSG00000251423	ENST00000637153.1	n.213+7480delA		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59796 AN: 151382 Hom.: 12158 Cov.: 0

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.401

GnomAD3 exomes AF: 0.413 AC: 99007 AN: 239752 Hom.: 20804 AF XY: 0.421 AC XY: 54642 AN XY: 129716

Gnomad AFR exome AF: 0.313

Gnomad AMR exome AF: 0.308

Gnomad ASJ exome AF: 0.371

Gnomad EAS exome AF: 0.250

Gnomad SAS exome AF: 0.484

Gnomad FIN exome AF: 0.487

Gnomad NFE exome AF: 0.455

Gnomad OTH exome AF: 0.409

GnomAD4 exome AF: 0.434 AC: 628653 AN: 1448288 Hom.: 137623 Cov.: 0 AF XY: 0.435 AC XY: 313552 AN XY: 720756

Gnomad4 AFR exome AF: 0.318

Gnomad4 AMR exome AF: 0.302

Gnomad4 ASJ exome AF: 0.361

Gnomad4 EAS exome AF: 0.261

Gnomad4 SAS exome AF: 0.469

Gnomad4 FIN exome AF: 0.479

Gnomad4 NFE exome AF: 0.447

Gnomad4 OTH exome AF: 0.418

GnomAD4 genome AF: 0.395 AC: 59856 AN: 151498 Hom.: 12176 Cov.: 0 AF XY: 0.394 AC XY: 29155 AN XY: 73988

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.405

Bravo AF: 0.374

Asia WGS AF: 0.381 AC: 1328 AN: 3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Primary ciliary dyskinesia Benign:4

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 23, 2019

Natera, Inc.

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jun 02, 2016

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

not specified Benign:3

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

-

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Primary ciliary dyskinesia 3 Benign:2

Nov 26, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 30, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:1

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 29089047, 25877373) -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs35398031; hg19: chr5-13868103;