NM_001277115.2:c.11202+13G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001277115.2(DNAH11):c.11202+13G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0698 in 1,609,544 control chromosomes in the GnomAD database, including 8,013 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 2625 hom., cov: 32)

Exomes 𝑓: 0.063 ( 5388 hom. )

Consequence

DNAH11
NM_001277115.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.334

Publications

5 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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 7-21854468-G-A is Benign according to our data. Variant chr7-21854468-G-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 163124.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH11	NM_001277115.2 link	c.11202+13G>A		intron_variant	Intron 68 of 81	ENST00000409508.8	NP_001264044.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
DNAH11	ENST00000409508.8 link	c.11202+13G>A	intron_variant	Intron 68 of 81	5	NM_001277115.2	ENSP00000475939.1
DNAH11	ENST00000421290.1 link	n.385+13G>A	intron_variant	Intron 3 of 3	4
DNAH11	ENST00000607413.5 link	n.465+13G>A	intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20711

AN:

151904

Hom.:

2621

Cov.:

show subpopulations

Gnomad AFR

AF:

0.330

Gnomad AMI

AF:

0.164

Gnomad AMR

AF:

0.0624

Gnomad ASJ

AF:

0.0465

Gnomad EAS

AF:

0.228

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.0628

Gnomad MID

AF:

0.119

Gnomad NFE

AF:

0.0439

Gnomad OTH

AF:

0.114

GnomAD2 exomes

AF:

0.0911

AC:

22470

AN:

246594

AF XY:

0.0896

show subpopulations

Gnomad AFR exome

AF:

0.334

Gnomad AMR exome

AF:

0.0425

Gnomad ASJ exome

AF:

0.0494

Gnomad EAS exome

AF:

0.227

Gnomad FIN exome

AF:

0.0646

Gnomad NFE exome

AF:

0.0480

Gnomad OTH exome

AF:

0.0743

GnomAD4 exome

AF:

0.0629

AC:

91644

AN:

1457522

Hom.:

5388

Cov.:

AF XY:

0.0642

AC XY:

46509

AN XY:

724790

show subpopulations

African (AFR)

AF:

0.336

AC:

11127

AN:

33144

American (AMR)

AF:

0.0442

AC:

1962

AN:

44362

Ashkenazi Jewish (ASJ)

AF:

0.0481

AC:

1255

AN:

26080

East Asian (EAS)

AF:

0.221

AC:

8732

AN:

39482

South Asian (SAS)

AF:

0.135

AC:

11465

AN:

84874

European-Finnish (FIN)

AF:

0.0610

AC:

3248

AN:

53250

Middle Eastern (MID)

AF:

0.0815

AC:

469

AN:

5758

European-Non Finnish (NFE)

AF:

0.0435

AC:

48252

AN:

1110378

Other (OTH)

AF:

0.0853

AC:

5134

AN:

60194

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

3748

7496

11245

14993

18741

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2076

4152

6228

8304

10380

<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:

0.137

AC:

20754

AN:

152022

Hom.:

2625

Cov.:

AF XY:

0.138

AC XY:

10223

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.330

AC:

13663

AN:

41396

American (AMR)

AF:

0.0623

AC:

953

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0465

AC:

161

AN:

3466

East Asian (EAS)

AF:

0.228

AC:

1178

AN:

5160

South Asian (SAS)

AF:

0.149

AC:

718

AN:

4808

European-Finnish (FIN)

AF:

0.0628

AC:

665

AN:

10588

Middle Eastern (MID)

AF:

0.128

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.0438

AC:

2981

AN:

67990

Other (OTH)

AF:

0.117

AC:

248

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

802

1604

2406

3208

4010

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<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:

0.0789

Hom.:

454

Bravo

AF:

0.144

Asia WGS

AF:

0.214

AC:

744

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

11202+13G>A in intron 68 of DNAH11: This variant is not expected to have clinica l significance because it is not located within the conserved splice consensus s equence. It has been identified in 32.3% (1157/3584) of African American chromos omes from a broad population by the NHLBI Exome Sequencing Project (http://evs.g s.washington.edu/EVS; dbSNP rs73279830). -

Primary ciliary dyskinesia

Benign:2

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

- -

not provided

Benign:2

Dec 31, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.1

(source)

DANN

Benign

0.32

PhyloP100

0.33

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