Variant 17-11854239-C-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.9744C>G(p.Pro3248=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 1,613,906 control chromosomes in the GnomAD database, including 141,008 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. P3248P) has been classified as Benign.

Frequency

Genomes: 𝑓 0.40 ( 12611 hom., cov: 32)

Exomes 𝑓: 0.42 ( 128397 hom. )

Consequence

DNAH9
NM_001372.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -4.91

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=-0.89).

BP6

Variant 17-11854239-C-G is Benign according to our data. Variant chr17-11854239-C-G is described in ClinVar as [Benign]. Clinvar id is 402782.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-4.91 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.54 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.9744C>G	p.Pro3248=	synonymous_variant	50/69	ENST00000262442.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH9	ENST00000262442.9 linkuse as main transcript	c.9744C>G	p.Pro3248=	synonymous_variant	50/69	1	NM_001372.4	P1	Q9NYC9-1
DNAH9	ENST00000454412.6 linkuse as main transcript	c.9744C>G	p.Pro3248=	synonymous_variant	50/68	5
DNAH9	ENST00000579703.1 linkuse as main transcript	c.186C>G	p.Pro62=	synonymous_variant	1/4	3
DNAH9	ENST00000578834.1 linkuse as main transcript	n.291C>G		non_coding_transcript_exon_variant	2/3	4

Frequencies

GnomAD3 genomes

AF:

0.401

AC:

60887

AN:

151906

Hom.:

12601

Cov.:

show subpopulations

Gnomad AFR

AF:

0.334

Gnomad AMI

AF:

0.347

Gnomad AMR

AF:

0.549

Gnomad ASJ

AF:

0.371

Gnomad EAS

AF:

0.366

Gnomad SAS

AF:

0.408

Gnomad FIN

AF:

0.411

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.411

Gnomad OTH

AF:

0.417

GnomAD3 exomes

AF:

0.432

AC:

108654

AN:

251438

Hom.:

24829

AF XY:

0.424

AC XY:

57571

AN XY:

135898

show subpopulations

Gnomad AFR exome

AF:

0.324

Gnomad AMR exome

AF:

0.663

Gnomad ASJ exome

AF:

0.352

Gnomad EAS exome

AF:

0.378

Gnomad SAS exome

AF:

0.408

Gnomad FIN exome

AF:

0.406

Gnomad NFE exome

AF:

0.405

Gnomad OTH exome

AF:

0.434

GnomAD4 exome

AF:

0.416

AC:

607421

AN:

1461882

Hom.:

128397

Cov.:

AF XY:

0.413

AC XY:

300160

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.322

Gnomad4 AMR exome

AF:

0.649

Gnomad4 ASJ exome

AF:

0.353

Gnomad4 EAS exome

AF:

0.356

Gnomad4 SAS exome

AF:

0.402

Gnomad4 FIN exome

AF:

0.402

Gnomad4 NFE exome

AF:

0.415

Gnomad4 OTH exome

AF:

0.400

GnomAD4 genome

AF:

0.401

AC:

60921

AN:

152024

Hom.:

12611

Cov.:

AF XY:

0.400

AC XY:

29734

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.333

Gnomad4 AMR

AF:

0.549

Gnomad4 ASJ

AF:

0.371

Gnomad4 EAS

AF:

0.367

Gnomad4 SAS

AF:

0.407

Gnomad4 FIN

AF:

0.411

Gnomad4 NFE

AF:

0.411

Gnomad4 OTH

AF:

0.415

Alfa

AF:

0.319

Hom.:

1327

Bravo

AF:

0.409

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	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: 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

-0.89

CADD

Benign

0.043

DANN

Benign

0.47

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