chr7-21735825-G-A

Position:

chr7-21735825-G-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001277115.2(DNAH11):c.7626G>A(p.Thr2542Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 1,610,410 control chromosomes in the GnomAD database, including 592,010 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T2542T) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.83 ( 53172 hom., cov: 32)

Exomes 𝑓: 0.86 ( 538838 hom. )

Consequence

DNAH11
NM_001277115.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -0.496

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 7-21735825-G-A is Benign according to our data. Variant chr7-21735825-G-A is described in ClinVar as [Benign]. Clinvar id is 163110.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-21735825-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.496 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH11	NM_001277115.2 link	c.7626G>A	p.Thr2542Thr	synonymous_variant	46/82	ENST00000409508.8	NP_001264044.1	Q96DT5Q96NT7H9NAJ8H9NAJ7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH11	ENST00000409508.8 link	c.7626G>A	p.Thr2542Thr	synonymous_variant	46/82	5	NM_001277115.2	ENSP00000475939.1		Q96DT5
DNAH11	ENST00000605912.1 link	c.186G>A	p.Thr62Thr	synonymous_variant	1/4	3		ENSP00000476068.1		U3KQN2

Frequencies

GnomAD3 genomes

AF:

0.833

AC:

126621

AN:

152026

Hom.:

53154

Cov.:

show subpopulations

Gnomad AFR

AF:

0.795

Gnomad AMI

AF:

0.863

Gnomad AMR

AF:

0.868

Gnomad ASJ

AF:

0.769

Gnomad EAS

AF:

0.527

Gnomad SAS

AF:

0.761

Gnomad FIN

AF:

0.904

Gnomad MID

AF:

0.797

Gnomad NFE

AF:

0.869

Gnomad OTH

AF:

0.817

GnomAD3 exomes

AF:

0.825

AC:

204412

AN:

247696

Hom.:

85552

AF XY:

0.827

AC XY:

111030

AN XY:

134334

show subpopulations

Gnomad AFR exome

AF:

0.796

Gnomad AMR exome

AF:

0.865

Gnomad ASJ exome

AF:

0.777

Gnomad EAS exome

AF:

0.519

Gnomad SAS exome

AF:

0.785

Gnomad FIN exome

AF:

0.900

Gnomad NFE exome

AF:

0.867

Gnomad OTH exome

AF:

0.828

GnomAD4 exome

AF:

0.857

AC:

1250264

AN:

1458266

Hom.:

538838

Cov.:

AF XY:

0.856

AC XY:

620240

AN XY:

724930

show subpopulations

Gnomad4 AFR exome

AF:

0.794

Gnomad4 AMR exome

AF:

0.867

Gnomad4 ASJ exome

AF:

0.775

Gnomad4 EAS exome

AF:

0.566

Gnomad4 SAS exome

AF:

0.790

Gnomad4 FIN exome

AF:

0.897

Gnomad4 NFE exome

AF:

0.877

Gnomad4 OTH exome

AF:

0.828

GnomAD4 genome

AF:

0.833

AC:

126695

AN:

152144

Hom.:

53172

Cov.:

AF XY:

0.832

AC XY:

61855

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.795

Gnomad4 AMR

AF:

0.868

Gnomad4 ASJ

AF:

0.769

Gnomad4 EAS

AF:

0.527

Gnomad4 SAS

AF:

0.760

Gnomad4 FIN

AF:

0.904

Gnomad4 NFE

AF:

0.869

Gnomad4 OTH

AF:

0.815

Alfa

AF:

0.856

Hom.:

97723

Bravo

AF:

0.839

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Feb 21, 2013	Thr2542Thr in exon 46 of DNAH11: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. It has been identified in 15.2% (589/3870) of African American chromosomes from a broad population by the NHLBI Exome Seque ncing Project (http://evs.gs.washington.edu/EVS; dbSNP rs2072221). -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Primary ciliary dyskinesia

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 03, 2025	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 14, 2016	- -

Primary ciliary dyskinesia 7

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 30, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 28, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

0.13

DANN

Benign

0.43

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