17-11834624-C-T

Variant names:

Variant summary

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

The NM_001372.4(DNAH9):c.9247-14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 1,611,902 control chromosomes in the GnomAD database, including 95,047 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.33 ( 8226 hom., cov: 32)

Exomes 𝑓: 0.34 ( 86821 hom. )

Consequence

DNAH9
NM_001372.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.323

Publications

5 publications found

Variant links:

Genes affected

DNAH9 (HGNC:2953): (dynein axonemal heavy chain 9) This gene encodes the heavy chain subunit of axonemal dynein, a large multi-subunit molecular motor. Axonemal dynein attaches to microtubules and hydrolyzes ATP to mediate the movement of cilia and flagella. The gene expresses at least two transcript variants; additional variants have been described, but their full length nature has not been determined. [provided by RefSeq, Jul 2008]

DNAH9 Gene-Disease associations (from GenCC):

ciliary dyskinesia, primary, 40
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia
primary ciliary dyskinesia
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
situs inversus
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
schizophrenia
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

DNAH9 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=-0.8).

BP6

Variant 17-11834624-C-T is Benign according to our data. Variant chr17-11834624-C-T is described in ClinVar as Benign. ClinVar VariationId is 402780.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH9	NM_001372.4 link	c.9247-14C>T		intron_variant	Intron 48 of 68	ENST00000262442.9	NP_001363.2	Q9NYC9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH9	ENST00000262442.9 link	c.9247-14C>T		intron_variant	Intron 48 of 68	1	NM_001372.4	ENSP00000262442.3		Q9NYC9-1
DNAH9	ENST00000454412.6 link	c.9247-14C>T		intron_variant	Intron 48 of 67	5		ENSP00000414874.2		E7EP17

Frequencies

GnomAD3 genomes

AF:

0.326

AC:

49449

AN:

151856

Hom.:

8206

Cov.:

show subpopulations

Gnomad AFR

AF:

0.263

Gnomad AMI

AF:

0.398

Gnomad AMR

AF:

0.407

Gnomad ASJ

AF:

0.340

Gnomad EAS

AF:

0.422

Gnomad SAS

AF:

0.389

Gnomad FIN

AF:

0.287

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.337

Gnomad OTH

AF:

0.343

GnomAD2 exomes

AF:

0.354

AC:

87841

AN:

248364

AF XY:

0.352

show subpopulations

Gnomad AFR exome

AF:

0.261

Gnomad AMR exome

AF:

0.454

Gnomad ASJ exome

AF:

0.326

Gnomad EAS exome

AF:

0.431

Gnomad FIN exome

AF:

0.292

Gnomad NFE exome

AF:

0.328

Gnomad OTH exome

AF:

0.359

GnomAD4 exome

AF:

0.343

AC:

500559

AN:

1459928

Hom.:

86821

Cov.:

AF XY:

0.343

AC XY:

248996

AN XY:

726144

show subpopulations

African (AFR)

AF:

0.261

AC:

8718

AN:

33462

American (AMR)

AF:

0.451

AC:

20067

AN:

44516

Ashkenazi Jewish (ASJ)

AF:

0.330

AC:

8600

AN:

26088

East Asian (EAS)

AF:

0.420

AC:

16664

AN:

39672

South Asian (SAS)

AF:

0.389

AC:

33463

AN:

86048

European-Finnish (FIN)

AF:

0.295

AC:

15670

AN:

53116

Middle Eastern (MID)

AF:

0.319

AC:

1840

AN:

5762

European-Non Finnish (NFE)

AF:

0.338

AC:

375177

AN:

1110916

Other (OTH)

AF:

0.337

AC:

20360

AN:

60348

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

16203

32406

48608

64811

81014

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12272

24544

36816

49088

61360

<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:

0.326

AC:

49493

AN:

151974

Hom.:

8226

Cov.:

AF XY:

0.324

AC XY:

24068

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.263

AC:

10896

AN:

41470

American (AMR)

AF:

0.408

AC:

6227

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.340

AC:

1177

AN:

3460

East Asian (EAS)

AF:

0.422

AC:

2173

AN:

5144

South Asian (SAS)

AF:

0.387

AC:

1865

AN:

4814

European-Finnish (FIN)

AF:

0.287

AC:

3037

AN:

10566

Middle Eastern (MID)

AF:

0.337

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.337

AC:

22929

AN:

67944

Other (OTH)

AF:

0.345

AC:

728

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1725

3450

5176

6901

8626

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

496

992

1488

1984

2480

<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:

0.333

Hom.:

1796

Bravo

AF:

0.335

Asia WGS

AF:

0.425

AC:

1478

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

May 11, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Ciliary dyskinesia, primary, 40

Benign:1

Jul 30, 2021

Genome-Nilou Lab

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

-0.80

CADD

Benign

9.3

(source)

DANN

Benign

0.59

PhyloP100

0.32

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