Variant rs60554135 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.9102+20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 1,046,238 control chromosomes in the GnomAD database, including 5,609 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 475 hom., cov: 24)

Exomes 𝑓: 0.11 ( 5134 hom. )

Consequence

DNAH11
NM_001277115.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0290

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=-0.78).

BP6

Variant 7-21765609-G-A is Benign according to our data. Variant chr7-21765609-G-A is described in ClinVar as [Benign]. Clinvar id is 257939.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-21765609-G-A is described in Lovd as [Benign].

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH11	NM_001277115.2 linkuse as main transcript	c.9102+20G>A		intron_variant		ENST00000409508.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH11	ENST00000409508.8 linkuse as main transcript	c.9102+20G>A		intron_variant		5	NM_001277115.2	P1

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

9475

AN:

86780

Hom.:

474

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0488

Gnomad AMI

AF:

0.122

Gnomad AMR

AF:

0.115

Gnomad ASJ

AF:

0.0779

Gnomad EAS

AF:

0.293

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.0889

Gnomad MID

AF:

0.202

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.154

GnomAD3 exomes

AF:

0.102

AC:

12758

AN:

125624

Hom.:

875

AF XY:

0.105

AC XY:

6916

AN XY:

66016

show subpopulations

Gnomad AFR exome

AF:

0.0313

Gnomad AMR exome

AF:

0.0528

Gnomad ASJ exome

AF:

0.0596

Gnomad EAS exome

AF:

0.278

Gnomad SAS exome

AF:

0.115

Gnomad FIN exome

AF:

0.0688

Gnomad NFE exome

AF:

0.0926

Gnomad OTH exome

AF:

0.104

GnomAD4 exome

AF:

0.107

AC:

102535

AN:

959374

Hom.:

5134

Cov.:

AF XY:

0.107

AC XY:

50816

AN XY:

475784

show subpopulations

Gnomad4 AFR exome

AF:

0.0311

Gnomad4 AMR exome

AF:

0.0569

Gnomad4 ASJ exome

AF:

0.0725

Gnomad4 EAS exome

AF:

0.288

Gnomad4 SAS exome

AF:

0.104

Gnomad4 FIN exome

AF:

0.0588

Gnomad4 NFE exome

AF:

0.105

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.109

AC:

9479

AN:

86864

Hom.:

475

Cov.:

AF XY:

0.112

AC XY:

4607

AN XY:

41210

show subpopulations

Gnomad4 AFR

AF:

0.0488

Gnomad4 AMR

AF:

0.115

Gnomad4 ASJ

AF:

0.0779

Gnomad4 EAS

AF:

0.293

Gnomad4 SAS

AF:

0.157

Gnomad4 FIN

AF:

0.0889

Gnomad4 NFE

AF:

0.125

Gnomad4 OTH

AF:

0.154

Alfa

AF:

0.0359

Hom.:

Bravo

AF:

0.0648

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 15, 2016

- -

Primary ciliary dyskinesia 7

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 30, 2021

- -

Primary ciliary dyskinesia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 24, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

2.0

DANN

Benign

0.72

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