Variant rs17144822 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_001277115.2(DNAH11):c.4726-15T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00807 in 1,519,198 control chromosomes in the GnomAD database, including 459 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0076 ( 41 hom., cov: 32)

Exomes 𝑓: 0.0081 ( 418 hom. )

Consequence

DNAH11
NM_001277115.2 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.573

Variant links:

Genes affected

DNAH11 (HGNC:2942): (dynein axonemal heavy chain 11) This gene encodes a ciliary outer dynein arm protein and is a member of the dynein heavy chain family. It is a microtubule-dependent motor ATPase and has been reported to be involved in the movement of respiratory cilia. Mutations in this gene have been implicated in causing Kartagener Syndrome (a combination of situs inversus totalis and Primary Ciliary Dyskinesia (PCD), also called Immotile Cilia Syndrome 1 (ICS1)) and male sterility. [provided by RefSeq, Mar 2013]

DNAH11 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 7-21637596-T-C is Benign according to our data. Variant chr7-21637596-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 226585.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-21637596-T-C is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH11	NM_001277115.2 linkuse as main transcript	c.4726-15T>C		intron_variant		ENST00000409508.8	NP_001264044.1	Q96DT5Q96NT7H9NAJ8H9NAJ7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH11	ENST00000409508.8 linkuse as main transcript	c.4726-15T>C		intron_variant		5	NM_001277115.2	ENSP00000475939.1		Q96DT5

Frequencies

GnomAD3 genomes

AF:

0.00765

AC:

1164

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0188

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.0649

Gnomad SAS

AF:

0.0760

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00123

Gnomad OTH

AF:

0.0101

GnomAD3 exomes

AF:

0.0204

AC:

3850

AN:

189010

Hom.:

131

AF XY:

0.0221

AC XY:

2218

AN XY:

100372

show subpopulations

Gnomad AFR exome

AF:

0.000917

Gnomad AMR exome

AF:

0.0330

Gnomad ASJ exome

AF:

0.00357

Gnomad EAS exome

AF:

0.0678

Gnomad SAS exome

AF:

0.0737

Gnomad FIN exome

AF:

0.0000541

Gnomad NFE exome

AF:

0.00129

Gnomad OTH exome

AF:

0.0133

GnomAD4 exome

AF:

0.00812

AC:

11100

AN:

1366886

Hom.:

418

Cov.:

AF XY:

0.00990

AC XY:

6730

AN XY:

679590

show subpopulations

Gnomad4 AFR exome

AF:

0.000702

Gnomad4 AMR exome

AF:

0.0299

Gnomad4 ASJ exome

AF:

0.00404

Gnomad4 EAS exome

AF:

0.0561

Gnomad4 SAS exome

AF:

0.0729

Gnomad4 FIN exome

AF:

0.000137

Gnomad4 NFE exome

AF:

0.00115

Gnomad4 OTH exome

AF:

0.0122

GnomAD4 genome

AF:

0.00763

AC:

1162

AN:

152312

Hom.:

Cov.:

AF XY:

0.00984

AC XY:

733

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.00120

Gnomad4 AMR

AF:

0.0188

Gnomad4 ASJ

AF:

0.00346

Gnomad4 EAS

AF:

0.0648

Gnomad4 SAS

AF:

0.0757

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.00123

Gnomad4 OTH

AF:

0.0104

Alfa

AF:

0.00366

Hom.:

Bravo

AF:

0.00726

Asia WGS

AF:

0.0620

AC:

219

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Feb 21, 2013	4726-15T>C in intron 26 of DNAH11: This variant is not expected to have clinical significance because it has been identified in 6.7% (12/178) of Japanese chromo somes from a broad population by the 1000 Genomes Project (http://www.ncbi.nlm.n ih.gov/projects/SNP; dbSNP rs17144822). -

Primary ciliary dyskinesia

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 14, 2016	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 16, 2019	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

8.4

DANN

Benign

0.53

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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