chr17-11930048-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001372.4(DNAH9):c.12060G>A(p.Thr4020Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 1,613,610 control chromosomes in the GnomAD database, including 77,315 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5567 hom., cov: 31)

Exomes 𝑓: 0.31 ( 71748 hom. )

Consequence

DNAH9
NM_001372.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -5.21

Publications

15 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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 17-11930048-G-A is Benign according to our data. Variant chr17-11930048-G-A is described in ClinVar as Benign. ClinVar VariationId is 402785.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-5.2 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001372.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAH9	NM_001372.4	MANE Select	c.12060G>A	p.Thr4020Thr	synonymous	Exon 63 of 69	NP_001363.2
	DNAH9	NM_004662.2		c.996G>A	p.Thr332Thr	synonymous	Exon 9 of 15	NP_004653.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
DNAH9	ENST00000262442.9	TSL:1 MANE Select	c.12060G>A	p.Thr4020Thr	synonymous	Exon 63 of 69	ENSP00000262442.3
DNAH9	ENST00000608377.5	TSL:1	c.996G>A	p.Thr332Thr	synonymous	Exon 9 of 15	ENSP00000476951.1
DNAH9	ENST00000396001.6	TSL:1	n.1523G>A		non_coding_transcript_exon	Exon 9 of 15

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38763

AN:

151868

Hom.:

5565

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.255

Gnomad AMR

AF:

0.252

Gnomad ASJ

AF:

0.353

Gnomad EAS

AF:

0.194

Gnomad SAS

AF:

0.317

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.306

Gnomad NFE

AF:

0.330

Gnomad OTH

AF:

0.291

GnomAD2 exomes

AF:

0.285

AC:

71418

AN:

250712

AF XY:

0.293

show subpopulations

Gnomad AFR exome

AF:

0.103

Gnomad AMR exome

AF:

0.199

Gnomad ASJ exome

AF:

0.361

Gnomad EAS exome

AF:

0.202

Gnomad FIN exome

AF:

0.317

Gnomad NFE exome

AF:

0.330

Gnomad OTH exome

AF:

0.317

GnomAD4 exome

AF:

0.309

AC:

451515

AN:

1461622

Hom.:

71748

Cov.:

AF XY:

0.312

AC XY:

226515

AN XY:

727104

show subpopulations

African (AFR)

AF:

0.0966

AC:

3234

AN:

33476

American (AMR)

AF:

0.209

AC:

9331

AN:

44698

Ashkenazi Jewish (ASJ)

AF:

0.357

AC:

9324

AN:

26126

East Asian (EAS)

AF:

0.164

AC:

6517

AN:

39692

South Asian (SAS)

AF:

0.313

AC:

27006

AN:

86240

European-Finnish (FIN)

AF:

0.318

AC:

16980

AN:

53396

Middle Eastern (MID)

AF:

0.343

AC:

1981

AN:

5768

European-Non Finnish (NFE)

AF:

0.323

AC:

358923

AN:

1111838

Other (OTH)

AF:

0.302

AC:

18219

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

17187

34375

51562

68750

85937

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11412

22824

34236

45648

57060

<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:

0.255

AC:

38764

AN:

151988

Hom.:

5567

Cov.:

AF XY:

0.256

AC XY:

18982

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.107

AC:

4448

AN:

41496

American (AMR)

AF:

0.253

AC:

3856

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.353

AC:

1225

AN:

3470

East Asian (EAS)

AF:

0.194

AC:

995

AN:

5134

South Asian (SAS)

AF:

0.317

AC:

1525

AN:

4808

European-Finnish (FIN)

AF:

0.318

AC:

3351

AN:

10554

Middle Eastern (MID)

AF:

0.303

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.330

AC:

22432

AN:

67952

Other (OTH)

AF:

0.290

AC:

610

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1387

2774

4161

5548

6935

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

412

824

1236

1648

2060

<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:

0.296

Hom.:

3120

Bravo

AF:

0.240

Asia WGS

AF:

0.237

AC:

821

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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

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: MAF

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

0.31

(source)

DANN

Benign

0.65

PhyloP100

-5.2

Mutation Taster

=89/11

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over