chr7-21558882-A-G

Position:

chr7-21558882-A-G

Variant summary

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

The NM_001277115.2(DNAH11):c.576A>G(p.Ile192Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 1,608,060 control chromosomes in the GnomAD database, including 555 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.012 ( 58 hom., cov: 33)

Exomes 𝑓: 0.010 ( 497 hom. )

Consequence

DNAH11
NM_001277115.2 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 1.95

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 (MetaRNN=0.0017288923).

BP6

Variant 7-21558882-A-G is Benign according to our data. Variant chr7-21558882-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 163094.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0742 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.576A>G	p.Ile192Met	missense_variant	3/82	ENST00000409508.8	NP_001264044.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH11	ENST00000409508.8 linkuse as main transcript	c.576A>G	p.Ile192Met	missense_variant	3/82	5	NM_001277115.2	ENSP00000475939	P1

Frequencies

GnomAD3 genomes

AF:

0.0120

AC:

1825

AN:

152230

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00248

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0504

Gnomad ASJ

AF:

0.0144

Gnomad EAS

AF:

0.0573

Gnomad SAS

AF:

0.0809

Gnomad FIN

AF:

0.000376

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00260

Gnomad OTH

AF:

0.0134

GnomAD3 exomes

AF:

0.0256

AC:

6106

AN:

238600

Hom.:

207

AF XY:

0.0262

AC XY:

3387

AN XY:

129100

show subpopulations

Gnomad AFR exome

AF:

0.00219

Gnomad AMR exome

AF:

0.0648

Gnomad ASJ exome

AF:

0.0163

Gnomad EAS exome

AF:

0.0622

Gnomad SAS exome

AF:

0.0788

Gnomad FIN exome

AF:

0.000188

Gnomad NFE exome

AF:

0.00251

Gnomad OTH exome

AF:

0.0199

GnomAD4 exome

AF:

0.0102

AC:

14879

AN:

1455712

Hom.:

497

Cov.:

AF XY:

0.0119

AC XY:

8617

AN XY:

723494

show subpopulations

Gnomad4 AFR exome

AF:

0.00129

Gnomad4 AMR exome

AF:

0.0618

Gnomad4 ASJ exome

AF:

0.0165

Gnomad4 EAS exome

AF:

0.0506

Gnomad4 SAS exome

AF:

0.0748

Gnomad4 FIN exome

AF:

0.000358

Gnomad4 NFE exome

AF:

0.00213

Gnomad4 OTH exome

AF:

0.0152

GnomAD4 genome

AF:

0.0120

AC:

1826

AN:

152348

Hom.:

Cov.:

AF XY:

0.0147

AC XY:

1098

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.00248

Gnomad4 AMR

AF:

0.0505

Gnomad4 ASJ

AF:

0.0144

Gnomad4 EAS

AF:

0.0573

Gnomad4 SAS

AF:

0.0808

Gnomad4 FIN

AF:

0.000376

Gnomad4 NFE

AF:

0.00260

Gnomad4 OTH

AF:

0.0137

Alfa

AF:

0.00525

Hom.:

Bravo

AF:

0.0124

TwinsUK

AF:

0.00243

AC:

ALSPAC

AF:

0.00104

AC:

ESP6500AA

AF:

0.00302

AC:

ESP6500EA

AF:

0.00429

AC:

ExAC

AF:

0.0234

AC:

2822

Asia WGS

AF:

0.0630

AC:

219

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Feb 21, 2013	Ile192Met in exon 3 of DNAH11: This variant is not expected to have clinical sig nificance because it has been identified in 7.3% (13/178) of Japanese chromosome s from a broad population by the 1000 Genomes Project (http://www.ncbi.nlm.nih.g ov/projects/SNP; dbSNP rs72655972). -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jun 27, 2014	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

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

AlphaMissense

Benign

0.079

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.053

.;.;T

Eigen

Benign

0.068

Eigen_PC

Benign

0.22

FATHMM_MKL

Benign

0.52

LIST_S2

Benign

0.61

T;T;T

MetaRNN

Benign

0.0017

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.6

.;.;L

MutationTaster

Benign

0.94

PrimateAI

Benign

0.27

PROVEAN

Benign

-1.2

.;N;.

REVEL

Benign

0.11

Sift

Benign

0.083

.;T;.

Polyphen

0.66

.;.;P

Vest4

0.049

ClinPred

0.020

GERP RS

4.9

Varity_R

0.073

gMVP

0.16

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

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