7-21619936-A-ATTAAT

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001277115.2(DNAH11):c.4378-17_4378-16insATTTA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 1,559,650 control chromosomes in the GnomAD database, including 142,372 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.45 ( 15627 hom., cov: 0)

Exomes 𝑓: 0.42 ( 126745 hom. )

Consequence

DNAH11
NM_001277115.2 intron

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 0.774

Publications

6 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 -16 ACMG points.

BP6

Variant 7-21619936-A-ATTAAT is Benign according to our data. Variant chr7-21619936-A-ATTAAT is described in ClinVar as [Likely_benign]. Clinvar id is 93688.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH11	NM_001277115.2 link	c.4378-17_4378-16insATTTA		intron_variant	Intron 24 of 81	ENST00000409508.8	NP_001264044.1	Q96DT5Q96NT7H9NAJ8H9NAJ7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH11	ENST00000409508.8 link	c.4378-20_4378-19insTTAAT		intron_variant	Intron 24 of 81	5	NM_001277115.2	ENSP00000475939.1		Q96DT5
DNAH11	ENST00000465593.1 link	n.404-20_404-19insTTAAT		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.446

AC:

67579

AN:

151354

Hom.:

15616

Cov.:

show subpopulations

Gnomad AFR

AF:

0.517

Gnomad AMI

AF:

0.393

Gnomad AMR

AF:

0.406

Gnomad ASJ

AF:

0.338

Gnomad EAS

AF:

0.760

Gnomad SAS

AF:

0.414

Gnomad FIN

AF:

0.376

Gnomad MID

AF:

0.303

Gnomad NFE

AF:

0.410

Gnomad OTH

AF:

0.425

GnomAD2 exomes

AF:

0.407

AC:

88438

AN:

217250

AF XY:

0.407

show subpopulations

Gnomad AFR exome

AF:

0.503

Gnomad AMR exome

AF:

0.297

Gnomad ASJ exome

AF:

0.331

Gnomad EAS exome

AF:

0.735

Gnomad FIN exome

AF:

0.379

Gnomad NFE exome

AF:

0.395

Gnomad OTH exome

AF:

0.382

GnomAD4 exome

AF:

0.417

AC:

587654

AN:

1408178

Hom.:

126745

Cov.:

AF XY:

0.416

AC XY:

291293

AN XY:

700296

show subpopulations

African (AFR)

AF:

0.496

AC:

15275

AN:

30766

American (AMR)

AF:

0.326

AC:

11667

AN:

35806

Ashkenazi Jewish (ASJ)

AF:

0.339

AC:

8528

AN:

25126

East Asian (EAS)

AF:

0.726

AC:

27623

AN:

38036

South Asian (SAS)

AF:

0.389

AC:

29992

AN:

77198

European-Finnish (FIN)

AF:

0.387

AC:

20554

AN:

53066

Middle Eastern (MID)

AF:

0.368

AC:

2088

AN:

5668

European-Non Finnish (NFE)

AF:

0.412

AC:

446850

AN:

1083968

Other (OTH)

AF:

0.428

AC:

25077

AN:

58544

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.431

Heterozygous variant carriers

15019

30037

45056

60074

75093

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13832

27664

41496

55328

69160

<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:

0.446

AC:

67631

AN:

151472

Hom.:

15627

Cov.:

AF XY:

0.444

AC XY:

32884

AN XY:

73988

show subpopulations

African (AFR)

AF:

0.517

AC:

21325

AN:

41254

American (AMR)

AF:

0.405

AC:

6177

AN:

15236

Ashkenazi Jewish (ASJ)

AF:

0.338

AC:

1168

AN:

3454

East Asian (EAS)

AF:

0.760

AC:

3869

AN:

5094

South Asian (SAS)

AF:

0.413

AC:

1988

AN:

4810

European-Finnish (FIN)

AF:

0.376

AC:

3947

AN:

10500

Middle Eastern (MID)

AF:

0.301

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.410

AC:

27817

AN:

67820

Other (OTH)

AF:

0.425

AC:

896

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1834

3668

5501

7335

9169

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

618

1236

1854

2472

3090

<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:

0.411

Hom.:

2196

Asia WGS

AF:

0.564

AC:

1962

AN:

3476

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:7

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

- -

May 09, 2013

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

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

Benign:2

Aug 12, 2015

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. -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Jul 17, 2020

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.77

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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