rs7260371

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_001256715.2(DNAAF3):c.790-14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 1,580,790 control chromosomes in the GnomAD database, including 25,997 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.24 ( 6171 hom., cov: 32)

Exomes 𝑓: 0.15 ( 19826 hom. )

Consequence

DNAAF3
NM_001256715.2 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:12

Conservation

PhyloP100: 0.698

Variant links:

Genes affected

DNAAF3 (HGNC:30492): (dynein axonemal assembly factor 3) The protein encoded by this gene is required for the assembly of axonemal inner and outer dynein arms and plays a role in assembling dynein complexes for transport into cilia. Defects in this gene are a cause of primary ciliary dyskinesia type 2 (CILD2). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]

DNAAF3 links:

DNAAF3-AS1 (HGNC:55292): (DNAAF3 antisense RNA 1)

DNAAF3-AS1 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=-0.8).

BP6

Variant 19-55161201-G-A is Benign according to our data. Variant chr19-55161201-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 257695.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-55161201-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAAF3	NM_001256715.2 link	c.790-14C>T		intron_variant	Intron 7 of 11	ENST00000524407.7	NP_001243644.1	Q8N9W5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAAF3	ENST00000524407.7 link	c.790-14C>T		intron_variant	Intron 7 of 11	1	NM_001256715.2	ENSP00000432046.3		Q8N9W5-1

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

36326

AN:

152062

Hom.:

6155

Cov.:

show subpopulations

Gnomad AFR

AF:

0.481

Gnomad AMI

AF:

0.145

Gnomad AMR

AF:

0.165

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.0819

Gnomad SAS

AF:

0.136

Gnomad FIN

AF:

0.0986

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.149

Gnomad OTH

AF:

0.239

GnomAD3 exomes

AF:

0.158

AC:

31552

AN:

199496

Hom.:

3312

AF XY:

0.157

AC XY:

16962

AN XY:

108356

show subpopulations

Gnomad AFR exome

AF:

0.491

Gnomad AMR exome

AF:

0.112

Gnomad ASJ exome

AF:

0.251

Gnomad EAS exome

AF:

0.0767

Gnomad SAS exome

AF:

0.135

Gnomad FIN exome

AF:

0.0973

Gnomad NFE exome

AF:

0.152

Gnomad OTH exome

AF:

0.191

GnomAD4 exome

AF:

0.154

AC:

220387

AN:

1428608

Hom.:

19826

Cov.:

AF XY:

0.153

AC XY:

108401

AN XY:

706786

show subpopulations

Gnomad4 AFR exome

AF:

0.495

Gnomad4 AMR exome

AF:

0.120

Gnomad4 ASJ exome

AF:

0.252

Gnomad4 EAS exome

AF:

0.0516

Gnomad4 SAS exome

AF:

0.137

Gnomad4 FIN exome

AF:

0.105

Gnomad4 NFE exome

AF:

0.148

Gnomad4 OTH exome

AF:

0.181

GnomAD4 genome

AF:

0.239

AC:

36388

AN:

152182

Hom.:

6171

Cov.:

AF XY:

0.231

AC XY:

17155

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.482

Gnomad4 AMR

AF:

0.164

Gnomad4 ASJ

AF:

0.256

Gnomad4 EAS

AF:

0.0817

Gnomad4 SAS

AF:

0.136

Gnomad4 FIN

AF:

0.0986

Gnomad4 NFE

AF:

0.149

Gnomad4 OTH

AF:

0.241

Alfa

AF:

0.203

Hom.:

771

Bravo

AF:

0.258

Asia WGS

AF:

0.164

AC:

569

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:12

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Primary ciliary dyskinesia 2

Benign:2

Sep 21, 2015

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

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: 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

- -

Jul 09, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Familial Hypertrophic Cardiomyopathy with Wolff-Parkinson-White Syndrome

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dilated Cardiomyopathy, Recessive

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hypertrophic cardiomyopathy

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Familial restrictive cardiomyopathy

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely 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

-0.80

CADD

Benign

7.5

DANN

Benign

0.86

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