rs73279830

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+13G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0698 in 1,609,544 control chromosomes in the GnomAD database, including 8,013 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 2625 hom., cov: 32)

Exomes 𝑓: 0.063 ( 5388 hom. )

Consequence

DNAH11
NM_001277115.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.334

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=-0.93).

BP6

Variant 7-21854468-G-A is Benign according to our data. Variant chr7-21854468-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 163124.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-21854468-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH11	NM_001277115.2 link	c.11202+13G>A		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+13G>A	intron_variant	Intron 68 of 81	5	NM_001277115.2	ENSP00000475939.1	Q96DT5
DNAH11	ENST00000421290.1 link	n.385+13G>A	intron_variant	Intron 3 of 3	4
DNAH11	ENST00000607413.5 link	n.465+13G>A	intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20711

AN:

151904

Hom.:

2621

Cov.:

show subpopulations

Gnomad AFR

AF:

0.330

Gnomad AMI

AF:

0.164

Gnomad AMR

AF:

0.0624

Gnomad ASJ

AF:

0.0465

Gnomad EAS

AF:

0.228

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.0628

Gnomad MID

AF:

0.119

Gnomad NFE

AF:

0.0439

Gnomad OTH

AF:

0.114

GnomAD3 exomes

AF:

0.0911

AC:

22470

AN:

246594

Hom.:

1885

AF XY:

0.0896

AC XY:

11978

AN XY:

133668

show subpopulations

Gnomad AFR exome

AF:

0.334

Gnomad AMR exome

AF:

0.0425

Gnomad ASJ exome

AF:

0.0494

Gnomad EAS exome

AF:

0.227

Gnomad SAS exome

AF:

0.139

Gnomad FIN exome

AF:

0.0646

Gnomad NFE exome

AF:

0.0480

Gnomad OTH exome

AF:

0.0743

GnomAD4 exome

AF:

0.0629

AC:

91644

AN:

1457522

Hom.:

5388

Cov.:

AF XY:

0.0642

AC XY:

46509

AN XY:

724790

show subpopulations

Gnomad4 AFR exome

AF:

0.336

Gnomad4 AMR exome

AF:

0.0442

Gnomad4 ASJ exome

AF:

0.0481

Gnomad4 EAS exome

AF:

0.221

Gnomad4 SAS exome

AF:

0.135

Gnomad4 FIN exome

AF:

0.0610

Gnomad4 NFE exome

AF:

0.0435

Gnomad4 OTH exome

AF:

0.0853

GnomAD4 genome

AF:

0.137

AC:

20754

AN:

152022

Hom.:

2625

Cov.:

AF XY:

0.138

AC XY:

10223

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.330

Gnomad4 AMR

AF:

0.0623

Gnomad4 ASJ

AF:

0.0465

Gnomad4 EAS

AF:

0.228

Gnomad4 SAS

AF:

0.149

Gnomad4 FIN

AF:

0.0628

Gnomad4 NFE

AF:

0.0438

Gnomad4 OTH

AF:

0.117

Alfa

AF:

0.0749

Hom.:

264

Bravo

AF:

0.144

Asia WGS

AF:

0.214

AC:

744

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

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+13G>A in intron 68 of DNAH11: This variant is not expected to have clinica l significance because it is not located within the conserved splice consensus s equence. It has been identified in 32.3% (1157/3584) of African American chromos omes from a broad population by the NHLBI Exome Sequencing Project (http://evs.g s.washington.edu/EVS; dbSNP rs73279830). -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Primary ciliary dyskinesia

Benign:2

Feb 03, 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

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Dec 31, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.1

DANN

Benign

0.32

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