Genetic Variant DNAH9:p.Asn2110Asn (chr17-11745015-C-T) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001372.4(DNAH9):c.6330C>T(p.Asn2110Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 1,613,622 control chromosomes in the GnomAD database, including 502,233 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.74 ( 42796 hom., cov: 32)

Exomes 𝑓: 0.79 ( 459437 hom. )

Consequence

DNAH9
NM_001372.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.437

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 17-11745015-C-T is Benign according to our data. Variant chr17-11745015-C-T is described in ClinVar as [Benign]. Clinvar id is 402777.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.437 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH9	NM_001372.4 link	c.6330C>T	p.Asn2110Asn	synonymous_variant	Exon 31 of 69	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.6330C>T	p.Asn2110Asn	synonymous_variant	Exon 31 of 69	1	NM_001372.4	ENSP00000262442.3		Q9NYC9-1
DNAH9	ENST00000454412.6 link	c.6330C>T	p.Asn2110Asn	synonymous_variant	Exon 31 of 68	5		ENSP00000414874.2		E7EP17

Frequencies

GnomAD3 genomes

AF:

0.745

AC:

113168

AN:

151924

Hom.:

42773

Cov.:

show subpopulations

Gnomad AFR

AF:

0.602

Gnomad AMI

AF:

0.768

Gnomad AMR

AF:

0.833

Gnomad ASJ

AF:

0.769

Gnomad EAS

AF:

0.916

Gnomad SAS

AF:

0.797

Gnomad FIN

AF:

0.723

Gnomad MID

AF:

0.763

Gnomad NFE

AF:

0.796

Gnomad OTH

AF:

0.778

GnomAD3 exomes

AF:

0.797

AC:

200377

AN:

251276

Hom.:

80594

AF XY:

0.797

AC XY:

108207

AN XY:

135812

show subpopulations

Gnomad AFR exome

AF:

0.599

Gnomad AMR exome

AF:

0.879

Gnomad ASJ exome

AF:

0.771

Gnomad EAS exome

AF:

0.912

Gnomad SAS exome

AF:

0.784

Gnomad FIN exome

AF:

0.728

Gnomad NFE exome

AF:

0.801

Gnomad OTH exome

AF:

0.801

GnomAD4 exome

AF:

0.791

AC:

1156618

AN:

1461580

Hom.:

459437

Cov.:

AF XY:

0.791

AC XY:

575471

AN XY:

727080

show subpopulations

Gnomad4 AFR exome

AF:

0.592

Gnomad4 AMR exome

AF:

0.873

Gnomad4 ASJ exome

AF:

0.776

Gnomad4 EAS exome

AF:

0.917

Gnomad4 SAS exome

AF:

0.787

Gnomad4 FIN exome

AF:

0.737

Gnomad4 NFE exome

AF:

0.794

Gnomad4 OTH exome

AF:

0.778

GnomAD4 genome

AF:

0.745

AC:

113240

AN:

152042

Hom.:

42796

Cov.:

AF XY:

0.746

AC XY:

55426

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.602

Gnomad4 AMR

AF:

0.833

Gnomad4 ASJ

AF:

0.769

Gnomad4 EAS

AF:

0.916

Gnomad4 SAS

AF:

0.797

Gnomad4 FIN

AF:

0.723

Gnomad4 NFE

AF:

0.796

Gnomad4 OTH

AF:

0.781

Alfa

AF:

0.791

Hom.:

94531

Bravo

AF:

0.747

Asia WGS

AF:

0.831

AC:

2890

AN:

3478

EpiCase

AF:

0.798

EpiControl

AF:

0.801

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Jan 24, 2020

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

-0.50

CADD

Benign

1.6

DANN

Benign

0.71

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over