17-11608140-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.429C>T(p.Pro143Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 1,594,930 control chromosomes in the GnomAD database, including 145,822 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 11811 hom., cov: 33)

Exomes 𝑓: 0.42 ( 134011 hom. )

Consequence

DNAH9
NM_001372.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.63

Publications

21 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=-0.75).

BP6

Variant 17-11608140-C-T is Benign according to our data. Variant chr17-11608140-C-T is described in ClinVar as [Benign]. Clinvar id is 402773.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH9	NM_001372.4 link	c.429C>T	p.Pro143Pro	synonymous_variant	Exon 2 of 69	ENST00000262442.9	NP_001363.2	Q9NYC9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
DNAH9	ENST00000262442.9 link	c.429C>T	p.Pro143Pro	synonymous_variant	Exon 2 of 69	1	NM_001372.4	ENSP00000262442.3	Q9NYC9-1
DNAH9	ENST00000579406.1 link	n.456C>T		non_coding_transcript_exon_variant	Exon 2 of 8	1
DNAH9	ENST00000454412.6 link	c.429C>T	p.Pro143Pro	synonymous_variant	Exon 2 of 68	5		ENSP00000414874.2	E7EP17
DNAH9	ENST00000579828.5 link	c.429C>T	p.Pro143Pro	synonymous_variant	Exon 2 of 4	2		ENSP00000463782.1	J3QQK8

Frequencies

GnomAD3 genomes

AF:

0.373

AC:

56743

AN:

152006

Hom.:

11802

Cov.:

show subpopulations

Gnomad AFR

AF:

0.203

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.525

Gnomad ASJ

AF:

0.479

Gnomad EAS

AF:

0.549

Gnomad SAS

AF:

0.620

Gnomad FIN

AF:

0.382

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.403

Gnomad OTH

AF:

0.422

GnomAD2 exomes

AF:

0.459

AC:

113315

AN:

246682

AF XY:

0.463

show subpopulations

Gnomad AFR exome

AF:

0.197

Gnomad AMR exome

AF:

0.633

Gnomad ASJ exome

AF:

0.480

Gnomad EAS exome

AF:

0.542

Gnomad FIN exome

AF:

0.379

Gnomad NFE exome

AF:

0.406

Gnomad OTH exome

AF:

0.454

GnomAD4 exome

AF:

0.422

AC:

609338

AN:

1442806

Hom.:

134011

Cov.:

AF XY:

0.427

AC XY:

304922

AN XY:

714354

show subpopulations

African (AFR)

AF:

0.191

AC:

6294

AN:

33028

American (AMR)

AF:

0.624

AC:

27100

AN:

43422

Ashkenazi Jewish (ASJ)

AF:

0.479

AC:

12328

AN:

25722

East Asian (EAS)

AF:

0.584

AC:

22861

AN:

39162

South Asian (SAS)

AF:

0.603

AC:

51174

AN:

84870

European-Finnish (FIN)

AF:

0.377

AC:

20040

AN:

53192

Middle Eastern (MID)

AF:

0.511

AC:

2911

AN:

5696

European-Non Finnish (NFE)

AF:

0.402

AC:

440955

AN:

1098204

Other (OTH)

AF:

0.431

AC:

25675

AN:

59510

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

15384

30768

46152

61536

76920

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.373

AC:

56771

AN:

152124

Hom.:

11811

Cov.:

AF XY:

0.380

AC XY:

28287

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.203

AC:

8435

AN:

41496

American (AMR)

AF:

0.526

AC:

8032

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.479

AC:

1662

AN:

3472

East Asian (EAS)

AF:

0.549

AC:

2840

AN:

5174

South Asian (SAS)

AF:

0.619

AC:

2991

AN:

4830

European-Finnish (FIN)

AF:

0.382

AC:

4034

AN:

10564

Middle Eastern (MID)

AF:

0.531

AC:

156

AN:

294

European-Non Finnish (NFE)

AF:

0.403

AC:

27413

AN:

67990

Other (OTH)

AF:

0.423

AC:

894

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1778

3557

5335

7114

8892

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.397

Hom.:

51909

Bravo

AF:

0.372

Asia WGS

AF:

0.559

AC:

1943

AN:

3478

EpiCase

AF:

0.417

EpiControl

AF:

0.420

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

May 04, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

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

- -

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

-0.75

CADD

Benign

0.64

(source)

DANN

Benign

0.47

PhyloP100

-1.6

Mutation Taster

=97/3

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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17-11608140-C-T

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