rs73279826

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

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

The NM_001277115.2(DNAH11):c.11202+7C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0248 in 1,611,074 control chromosomes in the GnomAD database, including 4,470 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.093 ( 1893 hom., cov: 32)

Exomes 𝑓: 0.018 ( 2577 hom. )

Consequence

DNAH11
NM_001277115.2 splice_region, intron

Scores

Splicing: ADA: 0.00009980

Clinical Significance

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

Conservation

PhyloP100: 0.127

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=-0.76).

BP6

Variant 7-21854462-C-A is Benign according to our data. Variant chr7-21854462-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 163123.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-21854462-C-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH11	NM_001277115.2 link	c.11202+7C>A		splice_region_variant, intron_variant	Intron 68 of 81	ENST00000409508.8	NP_001264044.1	Q96DT5Q96NT7H9NAJ8H9NAJ7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
DNAH11	ENST00000409508.8 link	c.11202+7C>A	splice_region_variant, intron_variant	Intron 68 of 81	5	NM_001277115.2	ENSP00000475939.1	Q96DT5
DNAH11	ENST00000421290.1 link	n.385+7C>A	splice_region_variant, intron_variant	Intron 3 of 3	4
DNAH11	ENST00000607413.5 link	n.465+7C>A	splice_region_variant, intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.0934

AC:

14182

AN:

151912

Hom.:

1894

Cov.:

show subpopulations

Gnomad AFR

AF:

0.285

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0348

Gnomad ASJ

AF:

0.00691

Gnomad EAS

AF:

0.220

Gnomad SAS

AF:

0.0118

Gnomad FIN

AF:

0.0303

Gnomad MID

AF:

0.0510

Gnomad NFE

AF:

0.00256

Gnomad OTH

AF:

0.0702

GnomAD3 exomes

AF:

0.0427

AC:

10571

AN:

247478

Hom.:

1099

AF XY:

0.0359

AC XY:

4812

AN XY:

134162

show subpopulations

Gnomad AFR exome

AF:

0.291

Gnomad AMR exome

AF:

0.0238

Gnomad ASJ exome

AF:

0.00847

Gnomad EAS exome

AF:

0.221

Gnomad SAS exome

AF:

0.00529

Gnomad FIN exome

AF:

0.0303

Gnomad NFE exome

AF:

0.00253

Gnomad OTH exome

AF:

0.0246

GnomAD4 exome

AF:

0.0177

AC:

25775

AN:

1459044

Hom.:

2577

Cov.:

AF XY:

0.0162

AC XY:

11742

AN XY:

725618

show subpopulations

Gnomad4 AFR exome

AF:

0.293

Gnomad4 AMR exome

AF:

0.0247

Gnomad4 ASJ exome

AF:

0.00824

Gnomad4 EAS exome

AF:

0.218

Gnomad4 SAS exome

AF:

0.00567

Gnomad4 FIN exome

AF:

0.0279

Gnomad4 NFE exome

AF:

0.00161

Gnomad4 OTH exome

AF:

0.0374

GnomAD4 genome

AF:

0.0933

AC:

14183

AN:

152030

Hom.:

1893

Cov.:

AF XY:

0.0933

AC XY:

6939

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.285

Gnomad4 AMR

AF:

0.0348

Gnomad4 ASJ

AF:

0.00691

Gnomad4 EAS

AF:

0.220

Gnomad4 SAS

AF:

0.0114

Gnomad4 FIN

AF:

0.0303

Gnomad4 NFE

AF:

0.00254

Gnomad4 OTH

AF:

0.0695

Alfa

AF:

0.0314

Hom.:

261

Bravo

AF:

0.105

Asia WGS

AF:

0.107

AC:

372

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

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 21, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

11202+7C>A in intron 68 of DNAH11: This variant is not expected to have clinical significance because it is not located within the conserved splice consensus se quence. It has been identified in 28.2% (1011/3586) of African American chromoso mes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs .washington.edu/EVS; dbSNP rs73279826). -

Primary ciliary dyskinesia

Benign:2

Feb 02, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

May 24, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.99

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00010

dbscSNV1_RF

Benign

0.0

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