rs1859887

Variant names:

Variant summary

Our verdict is Benign. Variant got -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

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=-0.7).

BP6

Variant 17-11930048-G-A is Benign according to our data. Variant chr17-11930048-G-A is described in ClinVar as [Benign]. Clinvar id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH9	NM_001372.4 link	c.12060G>A	p.Thr4020Thr	synonymous_variant	Exon 63 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.12060G>A	p.Thr4020Thr	synonymous_variant	Exon 63 of 69	1	NM_001372.4	ENSP00000262442.3	Q9NYC9-1
DNAH9	ENST00000608377.5 link	c.996G>A	p.Thr332Thr	synonymous_variant	Exon 9 of 15	1		ENSP00000476951.1	Q9NYC9-3
DNAH9	ENST00000396001.6 link	n.1523G>A		non_coding_transcript_exon_variant	Exon 9 of 15	1
DNAH9	ENST00000454412.6 link	c.11878-1966G>A		intron_variant	Intron 62 of 67	5		ENSP00000414874.2	E7EP17

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

GnomAD3 exomes

AF:

0.285

AC:

71418

AN:

250712

Hom.:

10952

AF XY:

0.293

AC XY:

39766

AN XY:

135494

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 SAS exome

AF:

0.305

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

Gnomad4 AFR exome

AF:

0.0966

Gnomad4 AMR exome

AF:

0.209

Gnomad4 ASJ exome

AF:

0.357

Gnomad4 EAS exome

AF:

0.164

Gnomad4 SAS exome

AF:

0.313

Gnomad4 FIN exome

AF:

0.318

Gnomad4 NFE exome

AF:

0.323

Gnomad4 OTH exome

AF:

0.302

GnomAD4 genome

AF:

0.255

AC:

38764

AN:

151988

Hom.:

5567

Cov.:

AF XY:

0.256

AC XY:

18982

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.107

Gnomad4 AMR

AF:

0.253

Gnomad4 ASJ

AF:

0.353

Gnomad4 EAS

AF:

0.194

Gnomad4 SAS

AF:

0.317

Gnomad4 FIN

AF:

0.318

Gnomad4 NFE

AF:

0.330

Gnomad4 OTH

AF:

0.290

Alfa

AF:

0.299

Hom.:

3111

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

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: MAF -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

0.31

DANN

Benign

0.65

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