Variant chr17-11929970-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001372.4(DNAH9):c.11982A>G(p.Pro3994=) 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 1,613,536 control chromosomes in the GnomAD database, including 77,602 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5576 hom., cov: 31)

Exomes 𝑓: 0.31 ( 72026 hom. )

Consequence

DNAH9
NM_001372.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.51

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=-0.79).

BP6

Variant 17-11929970-A-G is Benign according to our data. Variant chr17-11929970-A-G is described in ClinVar as [Benign]. Clinvar id is 402784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.51 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH9	NM_001372.4 linkuse as main transcript	c.11982A>G	p.Pro3994=	synonymous_variant	63/69	ENST00000262442.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH9	ENST00000262442.9 linkuse as main transcript	c.11982A>G	p.Pro3994=	synonymous_variant	63/69	1	NM_001372.4	P1	Q9NYC9-1
DNAH9	ENST00000608377.5 linkuse as main transcript	c.918A>G	p.Pro306=	synonymous_variant	9/15	1			Q9NYC9-3
DNAH9	ENST00000396001.6 linkuse as main transcript	n.1445A>G		non_coding_transcript_exon_variant	9/15	1
DNAH9	ENST00000454412.6 linkuse as main transcript	c.11878-2044A>G		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.256

AC:

38808

AN:

151868

Hom.:

5574

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.253

Gnomad ASJ

AF:

0.352

Gnomad EAS

AF:

0.194

Gnomad SAS

AF:

0.318

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.318

Gnomad NFE

AF:

0.331

Gnomad OTH

AF:

0.292

GnomAD3 exomes

AF:

0.285

AC:

71526

AN:

250620

Hom.:

10949

AF XY:

0.294

AC XY:

39843

AN XY:

135452

show subpopulations

Gnomad AFR exome

AF:

0.103

Gnomad AMR exome

AF:

0.200

Gnomad ASJ exome

AF:

0.360

Gnomad EAS exome

AF:

0.203

Gnomad SAS exome

AF:

0.305

Gnomad FIN exome

AF:

0.318

Gnomad NFE exome

AF:

0.331

Gnomad OTH exome

AF:

0.318

GnomAD4 exome

AF:

0.310

AC:

452413

AN:

1461548

Hom.:

72026

Cov.:

AF XY:

0.312

AC XY:

226953

AN XY:

727034

show subpopulations

Gnomad4 AFR exome

AF:

0.0971

Gnomad4 AMR exome

AF:

0.209

Gnomad4 ASJ exome

AF:

0.357

Gnomad4 EAS exome

AF:

0.165

Gnomad4 SAS exome

AF:

0.313

Gnomad4 FIN exome

AF:

0.319

Gnomad4 NFE exome

AF:

0.324

Gnomad4 OTH exome

AF:

0.302

GnomAD4 genome

AF:

0.255

AC:

38810

AN:

151988

Hom.:

5576

Cov.:

AF XY:

0.256

AC XY:

19004

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.107

Gnomad4 AMR

AF:

0.253

Gnomad4 ASJ

AF:

0.352

Gnomad4 EAS

AF:

0.194

Gnomad4 SAS

AF:

0.318

Gnomad4 FIN

AF:

0.317

Gnomad4 NFE

AF:

0.331

Gnomad4 OTH

AF:

0.291

Alfa

AF:

0.313

Hom.:

9820

Bravo

AF:

0.240

Asia WGS

AF:

0.238

AC:

826

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

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

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

-0.79

CADD

Benign

0.14

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