rs17144747

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001277115.2(DNAH11):c.2835A>G(p.Gln945Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0489 in 1,613,536 control chromosomes in the GnomAD database, including 2,471 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.069 ( 516 hom., cov: 32)

Exomes 𝑓: 0.047 ( 1955 hom. )

Consequence

DNAH11
NM_001277115.2 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 2.12

Variant links:

Genes affected

DNAH11 (HGNC:2942): (dynein axonemal heavy chain 11) This gene encodes a ciliary outer dynein arm protein and is a member of the dynein heavy chain family. It is a microtubule-dependent motor ATPase and has been reported to be involved in the movement of respiratory cilia. Mutations in this gene have been implicated in causing Kartagener Syndrome (a combination of situs inversus totalis and Primary Ciliary Dyskinesia (PCD), also called Immotile Cilia Syndrome 1 (ICS1)) and male sterility. [provided by RefSeq, Mar 2013]

DNAH11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant 7-21599954-A-G is Benign according to our data. Variant chr7-21599954-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 93685.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-21599954-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=2.12 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH11	NM_001277115.2 link	c.2835A>G	p.Gln945Gln	synonymous_variant	Exon 15 of 82	ENST00000409508.8	NP_001264044.1	Q96DT5Q96NT7H9NAJ8H9NAJ7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH11	ENST00000409508.8 link	c.2835A>G	p.Gln945Gln	synonymous_variant	Exon 15 of 82	5	NM_001277115.2	ENSP00000475939.1		Q96DT5

Frequencies

GnomAD3 genomes

AF:

0.0690

AC:

10500

AN:

152072

Hom.:

510

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.0504

Gnomad AMR

AF:

0.0360

Gnomad ASJ

AF:

0.0429

Gnomad EAS

AF:

0.0198

Gnomad SAS

AF:

0.0622

Gnomad FIN

AF:

0.0349

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0453

Gnomad OTH

AF:

0.0593

GnomAD3 exomes

AF:

0.0469

AC:

11660

AN:

248418

Hom.:

390

AF XY:

0.0467

AC XY:

6295

AN XY:

134766

show subpopulations

Gnomad AFR exome

AF:

0.141

Gnomad AMR exome

AF:

0.0194

Gnomad ASJ exome

AF:

0.0485

Gnomad EAS exome

AF:

0.0267

Gnomad SAS exome

AF:

0.0548

Gnomad FIN exome

AF:

0.0345

Gnomad NFE exome

AF:

0.0460

Gnomad OTH exome

AF:

0.0413

GnomAD4 exome

AF:

0.0467

AC:

68309

AN:

1461346

Hom.:

1955

Cov.:

AF XY:

0.0467

AC XY:

33936

AN XY:

726936

show subpopulations

Gnomad4 AFR exome

AF:

0.146

Gnomad4 AMR exome

AF:

0.0216

Gnomad4 ASJ exome

AF:

0.0461

Gnomad4 EAS exome

AF:

0.0154

Gnomad4 SAS exome

AF:

0.0564

Gnomad4 FIN exome

AF:

0.0365

Gnomad4 NFE exome

AF:

0.0454

Gnomad4 OTH exome

AF:

0.0517

GnomAD4 genome

AF:

0.0692

AC:

10527

AN:

152190

Hom.:

516

Cov.:

AF XY:

0.0673

AC XY:

5009

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.140

Gnomad4 AMR

AF:

0.0358

Gnomad4 ASJ

AF:

0.0429

Gnomad4 EAS

AF:

0.0199

Gnomad4 SAS

AF:

0.0622

Gnomad4 FIN

AF:

0.0349

Gnomad4 NFE

AF:

0.0453

Gnomad4 OTH

AF:

0.0587

Alfa

AF:

0.0521

Hom.:

359

Bravo

AF:

0.0722

Asia WGS

AF:

0.0480

AC:

168

AN:

3478

EpiCase

AF:

0.0417

EpiControl

AF:

0.0419

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 05, 2015

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 21, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Gln945Gln in exon 15 of DNAH11: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue and is not located wi thin the splice consensus sequence. It has been identified in 12.2% (449/3690) o f African American chromosomes from a broad population by the NHLBI Exome Sequen cing Project (http://evs.gs.washington.edu/EVS; dbSNP rs17144747). -

Primary ciliary dyskinesia

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Dec 31, 2018

GeneDx

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

-0.52

CADD

Benign

DANN

Benign

0.53

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.17

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