7-21705443-A-G

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.6469-17A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 1,612,334 control chromosomes in the GnomAD database, including 86,466 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.43 ( 19566 hom., cov: 33)

Exomes 𝑓: 0.26 ( 66900 hom. )

Consequence

DNAH11
NM_001277115.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.349

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 7-21705443-A-G is Benign according to our data. Variant chr7-21705443-A-G is described in ClinVar as Benign. ClinVar VariationId is 257920.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH11	NM_001277115.2 link	c.6469-17A>G		intron_variant	Intron 38 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.6469-17A>G		intron_variant	Intron 38 of 81	5	NM_001277115.2	ENSP00000475939.1		Q96DT5

Frequencies

GnomAD3 genomes

AF:

0.429

AC:

65257

AN:

152010

Hom.:

19511

Cov.:

show subpopulations

Gnomad AFR

AF:

0.814

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.443

Gnomad ASJ

AF:

0.201

Gnomad EAS

AF:

0.742

Gnomad SAS

AF:

0.455

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.205

Gnomad OTH

AF:

0.365

GnomAD2 exomes

AF:

0.366

AC:

90798

AN:

247876

AF XY:

0.350

show subpopulations

Gnomad AFR exome

AF:

0.832

Gnomad AMR exome

AF:

0.536

Gnomad ASJ exome

AF:

0.195

Gnomad EAS exome

AF:

0.744

Gnomad FIN exome

AF:

0.297

Gnomad NFE exome

AF:

0.204

Gnomad OTH exome

AF:

0.292

GnomAD4 exome

AF:

0.262

AC:

382811

AN:

1460206

Hom.:

66900

Cov.:

AF XY:

0.264

AC XY:

191512

AN XY:

726344

show subpopulations

African (AFR)

AF:

0.841

AC:

28100

AN:

33422

American (AMR)

AF:

0.524

AC:

23307

AN:

44512

Ashkenazi Jewish (ASJ)

AF:

0.196

AC:

5117

AN:

26084

East Asian (EAS)

AF:

0.767

AC:

30396

AN:

39652

South Asian (SAS)

AF:

0.431

AC:

37113

AN:

86066

European-Finnish (FIN)

AF:

0.290

AC:

15449

AN:

53334

Middle Eastern (MID)

AF:

0.311

AC:

1790

AN:

5756

European-Non Finnish (NFE)

AF:

0.201

AC:

223205

AN:

1111080

Other (OTH)

AF:

0.304

AC:

18334

AN:

60300

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

13051

26101

39152

52202

65253

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8442

16884

25326

33768

42210

<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:

0.430

AC:

65382

AN:

152128

Hom.:

19566

Cov.:

AF XY:

0.437

AC XY:

32487

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.814

AC:

33807

AN:

41512

American (AMR)

AF:

0.443

AC:

6773

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.201

AC:

697

AN:

3470

East Asian (EAS)

AF:

0.742

AC:

3839

AN:

5176

South Asian (SAS)

AF:

0.456

AC:

2198

AN:

4816

European-Finnish (FIN)

AF:

0.295

AC:

3114

AN:

10550

Middle Eastern (MID)

AF:

0.306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.205

AC:

13949

AN:

68002

Other (OTH)

AF:

0.368

AC:

779

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1356

2712

4069

5425

6781

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

540

1080

1620

2160

2700

<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:

0.286

Hom.:

11895

Bravo

AF:

0.456

Asia WGS

AF:

0.609

AC:

2115

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

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

- -

Primary ciliary dyskinesia

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

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

-0.90

CADD

Benign

0.47

(source)

DANN

Benign

0.27

PhyloP100

-0.35

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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