rs11768670

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001277115.2(DNAH11):c.7335G>A(p.Ser2445Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 1,607,404 control chromosomes in the GnomAD database, including 40,519 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S2445S) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.20 ( 3233 hom., cov: 32)

Exomes 𝑓: 0.22 ( 37286 hom. )

Consequence

DNAH11
NM_001277115.2 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -0.613

Publications

9 publications found

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 Gene-Disease associations (from GenCC):

primary ciliary dyskinesia 7
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), ClinGen
primary ciliary dyskinesia
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

DNAH11 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.32).

BP6

Variant 7-21725879-G-A is Benign according to our data. Variant chr7-21725879-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 178728.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.613 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH11	NM_001277115.2 link	c.7335G>A	p.Ser2445Ser	synonymous_variant	Exon 45 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.7335G>A	p.Ser2445Ser	synonymous_variant	Exon 45 of 82	5	NM_001277115.2	ENSP00000475939.1		Q96DT5

Frequencies

GnomAD3 genomes

AF:

0.197

AC:

29924

AN:

151894

Hom.:

3233

Cov.:

show subpopulations

Gnomad AFR

AF:

0.141

Gnomad AMI

AF:

0.212

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.209

Gnomad EAS

AF:

0.0566

Gnomad SAS

AF:

0.0963

Gnomad FIN

AF:

0.272

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.195

GnomAD2 exomes

AF:

0.189

AC:

45161

AN:

238888

AF XY:

0.190

show subpopulations

Gnomad AFR exome

AF:

0.137

Gnomad AMR exome

AF:

0.135

Gnomad ASJ exome

AF:

0.212

Gnomad EAS exome

AF:

0.0521

Gnomad FIN exome

AF:

0.270

Gnomad NFE exome

AF:

0.240

Gnomad OTH exome

AF:

0.206

GnomAD4 exome

AF:

0.221

AC:

321286

AN:

1455392

Hom.:

37286

Cov.:

AF XY:

0.218

AC XY:

157476

AN XY:

723162

show subpopulations

African (AFR)

AF:

0.133

AC:

4435

AN:

33428

American (AMR)

AF:

0.143

AC:

6276

AN:

43978

Ashkenazi Jewish (ASJ)

AF:

0.213

AC:

5531

AN:

25962

East Asian (EAS)

AF:

0.0704

AC:

2788

AN:

39618

South Asian (SAS)

AF:

0.105

AC:

8917

AN:

84728

European-Finnish (FIN)

AF:

0.269

AC:

14273

AN:

53118

Middle Eastern (MID)

AF:

0.195

AC:

1122

AN:

5764

European-Non Finnish (NFE)

AF:

0.240

AC:

265709

AN:

1108660

Other (OTH)

AF:

0.203

AC:

12235

AN:

60136

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

12782

25565

38347

51130

63912

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.197

AC:

29926

AN:

152012

Hom.:

3233

Cov.:

AF XY:

0.195

AC XY:

14484

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.140

AC:

5819

AN:

41474

American (AMR)

AF:

0.183

AC:

2787

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.209

AC:

726

AN:

3468

East Asian (EAS)

AF:

0.0567

AC:

294

AN:

5186

South Asian (SAS)

AF:

0.0961

AC:

463

AN:

4816

European-Finnish (FIN)

AF:

0.272

AC:

2861

AN:

10514

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.240

AC:

16321

AN:

67968

Other (OTH)

AF:

0.193

AC:

407

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1211

2422

3634

4845

6056

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.218

Hom.:

16941

Bravo

AF:

0.189

Asia WGS

AF:

0.0830

AC:

290

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

PreventionGenetics, part of Exact Sciences

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

Ser2445Ser in exon 45 of DNAH11: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. It has been identified in 23.6% (1930/8180) of European American chromosomes from a broad population by the NHLBI Exome Seq uencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs11768670). -

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

- -

Nov 10, 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

-0.32

CADD

Benign

8.3

(source)

DANN

Benign

0.75

PhyloP100

-0.61

Mutation Taster

=98/2

polymorphism (auto)

(source)

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

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rs11768670

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over