Variant 17-11834624-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001372.4(DNAH9):c.9247-14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 1,611,902 control chromosomes in the GnomAD database, including 95,047 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.33 ( 8226 hom., cov: 32)

Exomes 𝑓: 0.34 ( 86821 hom. )

Consequence

DNAH9
NM_001372.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.323

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 17-11834624-C-T is Benign according to our data. Variant chr17-11834624-C-T is described in ClinVar as [Benign]. Clinvar id is 402780.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH9	NM_001372.4 linkuse as main transcript	c.9247-14C>T		intron_variant		ENST00000262442.9	NP_001363.2	Q9NYC9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH9	ENST00000262442.9 linkuse as main transcript	c.9247-14C>T		intron_variant		1	NM_001372.4	ENSP00000262442.3		Q9NYC9-1
DNAH9	ENST00000454412.6 linkuse as main transcript	c.9247-14C>T		intron_variant		5		ENSP00000414874.2		E7EP17

Frequencies

GnomAD3 genomes

AF:

0.326

AC:

49449

AN:

151856

Hom.:

8206

Cov.:

show subpopulations

Gnomad AFR

AF:

0.263

Gnomad AMI

AF:

0.398

Gnomad AMR

AF:

0.407

Gnomad ASJ

AF:

0.340

Gnomad EAS

AF:

0.422

Gnomad SAS

AF:

0.389

Gnomad FIN

AF:

0.287

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.337

Gnomad OTH

AF:

0.343

GnomAD3 exomes

AF:

0.354

AC:

87841

AN:

248364

Hom.:

15554

AF XY:

0.352

AC XY:

47288

AN XY:

134308

show subpopulations

Gnomad AFR exome

AF:

0.261

Gnomad AMR exome

AF:

0.454

Gnomad ASJ exome

AF:

0.326

Gnomad EAS exome

AF:

0.431

Gnomad SAS exome

AF:

0.390

Gnomad FIN exome

AF:

0.292

Gnomad NFE exome

AF:

0.328

Gnomad OTH exome

AF:

0.359

GnomAD4 exome

AF:

0.343

AC:

500559

AN:

1459928

Hom.:

86821

Cov.:

AF XY:

0.343

AC XY:

248996

AN XY:

726144

show subpopulations

Gnomad4 AFR exome

AF:

0.261

Gnomad4 AMR exome

AF:

0.451

Gnomad4 ASJ exome

AF:

0.330

Gnomad4 EAS exome

AF:

0.420

Gnomad4 SAS exome

AF:

0.389

Gnomad4 FIN exome

AF:

0.295

Gnomad4 NFE exome

AF:

0.338

Gnomad4 OTH exome

AF:

0.337

GnomAD4 genome

AF:

0.326

AC:

49493

AN:

151974

Hom.:

8226

Cov.:

AF XY:

0.324

AC XY:

24068

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.263

Gnomad4 AMR

AF:

0.408

Gnomad4 ASJ

AF:

0.340

Gnomad4 EAS

AF:

0.422

Gnomad4 SAS

AF:

0.387

Gnomad4 FIN

AF:

0.287

Gnomad4 NFE

AF:

0.337

Gnomad4 OTH

AF:

0.345

Alfa

AF:

0.333

Hom.:

1796

Bravo

AF:

0.335

Asia WGS

AF:

0.425

AC:

1478

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

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 11, 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: Frequency -

Ciliary dyskinesia, primary, 40

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 30, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

9.3

DANN

Benign

0.59

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