dbSNP rs5882827: DNAH11:c.11691-20dupT (chr7-21867834-G-GT) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_001277115.2(DNAH11):c.11691-20dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 1,548,976 control chromosomes in the GnomAD database, including 377,222 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.54 ( 26740 hom., cov: 0)

Exomes 𝑓: 0.70 ( 350482 hom. )

Consequence

DNAH11
NM_001277115.2 intron

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:3

Conservation

PhyloP100: 0.558

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 -9 ACMG points.

BP6

Variant 7-21867834-G-GT is Benign according to our data. Variant chr7-21867834-G-GT is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 198650.We mark this variant Likely_benign, oryginal submissions are: {Benign=2, Uncertain_significance=1}.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH11	NM_001277115.2 link	c.11691-20dupT		intron_variant	Intron 71 of 81	ENST00000409508.8	NP_001264044.1	Q96DT5Q96NT7H9NAJ8H9NAJ7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH11	ENST00000409508.8 link	c.11691-25_11691-24insT		intron_variant	Intron 71 of 81	5	NM_001277115.2	ENSP00000475939.1		Q96DT5

Frequencies

GnomAD3 genomes

AF:

0.545

AC:

82033

AN:

150502

Hom.:

26744

Cov.:

show subpopulations

Gnomad AFR

AF:

0.188

Gnomad AMI

AF:

0.707

Gnomad AMR

AF:

0.554

Gnomad ASJ

AF:

0.721

Gnomad EAS

AF:

0.348

Gnomad SAS

AF:

0.474

Gnomad FIN

AF:

0.707

Gnomad MID

AF:

0.595

Gnomad NFE

AF:

0.738

Gnomad OTH

AF:

0.585

GnomAD3 exomes

AF:

0.600

AC:

96921

AN:

161480

Hom.:

31383

AF XY:

0.604

AC XY:

51498

AN XY:

85224

show subpopulations

Gnomad AFR exome

AF:

0.169

Gnomad AMR exome

AF:

0.493

Gnomad ASJ exome

AF:

0.713

Gnomad EAS exome

AF:

0.357

Gnomad SAS exome

AF:

0.495

Gnomad FIN exome

AF:

0.694

Gnomad NFE exome

AF:

0.736

Gnomad OTH exome

AF:

0.646

GnomAD4 exome

AF:

0.696

AC:

973546

AN:

1398364

Hom.:

350482

Cov.:

AF XY:

0.692

AC XY:

477394

AN XY:

690154

show subpopulations

Gnomad4 AFR exome

AF:

0.163

Gnomad4 AMR exome

AF:

0.507

Gnomad4 ASJ exome

AF:

0.715

Gnomad4 EAS exome

AF:

0.363

Gnomad4 SAS exome

AF:

0.493

Gnomad4 FIN exome

AF:

0.701

Gnomad4 NFE exome

AF:

0.747

Gnomad4 OTH exome

AF:

0.647

GnomAD4 genome

AF:

0.545

AC:

82017

AN:

150612

Hom.:

26740

Cov.:

AF XY:

0.541

AC XY:

39780

AN XY:

73592

show subpopulations

Gnomad4 AFR

AF:

0.188

Gnomad4 AMR

AF:

0.553

Gnomad4 ASJ

AF:

0.721

Gnomad4 EAS

AF:

0.347

Gnomad4 SAS

AF:

0.474

Gnomad4 FIN

AF:

0.707

Gnomad4 NFE

AF:

0.738

Gnomad4 OTH

AF:

0.580

Alfa

AF:

0.637

Hom.:

5572

Bravo

AF:

0.513

Asia WGS

AF:

0.362

AC:

1261

AN:

3476

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:3

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Uncertain:1Benign:1

Feb 21, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 29, 2014

Eurofins Ntd Llc (ga)

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

DNAH11-related disorder

Benign:1

Apr 07, 2021

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Primary ciliary dyskinesia 7

Benign:1

Jul 30, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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