rs3827657

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001277115.2(DNAH11):c.3630G>A(p.Gln1210Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 1,583,142 control chromosomes in the GnomAD database, including 521,196 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.79 ( 47148 hom., cov: 31)

Exomes 𝑓: 0.81 ( 474048 hom. )

Consequence

DNAH11
NM_001277115.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -0.499

Publications

22 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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 7-21601600-G-A is Benign according to our data. Variant chr7-21601600-G-A is described in ClinVar as Benign. ClinVar VariationId is 163102.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.499 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH11	NM_001277115.2 link	c.3630G>A	p.Gln1210Gln	synonymous_variant	Exon 18 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.3630G>A	p.Gln1210Gln	synonymous_variant	Exon 18 of 82	5	NM_001277115.2	ENSP00000475939.1		Q96DT5

Frequencies

GnomAD3 genomes

AF:

0.786

AC:

119404

AN:

151952

Hom.:

47106

Cov.:

show subpopulations

Gnomad AFR

AF:

0.740

Gnomad AMI

AF:

0.857

Gnomad AMR

AF:

0.712

Gnomad ASJ

AF:

0.690

Gnomad EAS

AF:

0.801

Gnomad SAS

AF:

0.701

Gnomad FIN

AF:

0.820

Gnomad MID

AF:

0.699

Gnomad NFE

AF:

0.834

Gnomad OTH

AF:

0.787

GnomAD2 exomes

AF:

0.772

AC:

182139

AN:

235816

AF XY:

0.774

show subpopulations

Gnomad AFR exome

AF:

0.732

Gnomad AMR exome

AF:

0.649

Gnomad ASJ exome

AF:

0.686

Gnomad EAS exome

AF:

0.792

Gnomad FIN exome

AF:

0.826

Gnomad NFE exome

AF:

0.830

Gnomad OTH exome

AF:

0.781

GnomAD4 exome

AF:

0.812

AC:

1162082

AN:

1431072

Hom.:

474048

Cov.:

AF XY:

0.808

AC XY:

570938

AN XY:

706308

show subpopulations

African (AFR)

AF:

0.724

AC:

23667

AN:

32678

American (AMR)

AF:

0.657

AC:

27562

AN:

41938

Ashkenazi Jewish (ASJ)

AF:

0.684

AC:

17415

AN:

25478

East Asian (EAS)

AF:

0.759

AC:

29597

AN:

38984

South Asian (SAS)

AF:

0.691

AC:

57158

AN:

82770

European-Finnish (FIN)

AF:

0.832

AC:

43966

AN:

52848

Middle Eastern (MID)

AF:

0.691

AC:

3911

AN:

5664

European-Non Finnish (NFE)

AF:

0.835

AC:

911467

AN:

1091772

Other (OTH)

AF:

0.803

AC:

47339

AN:

58940

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

10172

20344

30516

40688

50860

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20938

41876

62814

83752

104690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.786

AC:

119496

AN:

152070

Hom.:

47148

Cov.:

AF XY:

0.780

AC XY:

57984

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.741

AC:

30708

AN:

41468

American (AMR)

AF:

0.711

AC:

10861

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.690

AC:

2391

AN:

3466

East Asian (EAS)

AF:

0.801

AC:

4133

AN:

5160

South Asian (SAS)

AF:

0.701

AC:

3379

AN:

4820

European-Finnish (FIN)

AF:

0.820

AC:

8666

AN:

10564

Middle Eastern (MID)

AF:

0.707

AC:

208

AN:

294

European-Non Finnish (NFE)

AF:

0.834

AC:

56702

AN:

68000

Other (OTH)

AF:

0.790

AC:

1666

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1314

2628

3942

5256

6570

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

866

1732

2598

3464

4330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.806

Hom.:

91107

Bravo

AF:

0.776

Asia WGS

AF:

0.798

AC:

2778

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

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

- -

Feb 21, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Gln1210Gln in exon 18 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 25.3% (958/3782) of African American chromosomes from a broad population by the NHLBI Exome Seque ncing Project (http://evs.gs.washington.edu/EVS; dbSNP rs3827657). -

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

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:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Primary ciliary dyskinesia 7

Benign:1

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

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

1.4

(source)

DANN

Benign

0.47

PhyloP100

-0.50

Mutation Taster

=100/0

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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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