Variant 2-84528872-A-AT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001370.2(DNAH6):c.400-21dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.65 ( 32476 hom., cov: 0)

Exomes 𝑓: 0.49 ( 70136 hom. )

Failed GnomAD Quality Control

Consequence

DNAH6
NM_001370.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.797

Variant links:

Genes affected

DNAH6 (HGNC:2951): (dynein axonemal heavy chain 6) This gene belongs to the dynein family, whose members encode large proteins that are constituents of the microtubule-associated motor protein complex. This complex is composed of dynein heavy, intermediate and light chains, which can be axonemal or cytoplasmic. This protein is an axonemal dynein heavy chain. It is involved in producing force for ciliary beating by using energy from ATP hydrolysis. Mutations in this gene may cause primary ciliary dyskinesia (PCD) as well as heterotaxy. [provided by RefSeq, Jun 2016]

DNAH6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 2-84528872-A-AT is Benign according to our data. Variant chr2-84528872-A-AT is described in ClinVar as [Benign]. Clinvar id is 1281178.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH6	NM_001370.2 link	c.400-21dupT		intron_variant		ENST00000389394.8	NP_001361.1	Q9C0G6-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
DNAH6	ENST00000389394.8 link	c.400-32_400-31insT	intron_variant	5	NM_001370.2	ENSP00000374045.3	Q9C0G6-1
DNAH6	ENST00000494025.1 link	n.229+10821_229+10822insT	intron_variant	1
DNAH6	ENST00000468661.1 link	n.454+3134_454+3135insT	intron_variant	4
DNAH6	ENST00000476689.5 link	n.536+3134_536+3135insT	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.655

AC:

97148

AN:

148396

Hom.:

32464

Cov.:

show subpopulations

Gnomad AFR

AF:

0.757

Gnomad AMI

AF:

0.493

Gnomad AMR

AF:

0.671

Gnomad ASJ

AF:

0.698

Gnomad EAS

AF:

0.830

Gnomad SAS

AF:

0.654

Gnomad FIN

AF:

0.590

Gnomad MID

AF:

0.705

Gnomad NFE

AF:

0.585

Gnomad OTH

AF:

0.678

GnomAD3 exomes

AF:

0.508

AC:

46245

AN:

91098

Hom.:

5386

AF XY:

0.501

AC XY:

24176

AN XY:

48272

show subpopulations

Gnomad AFR exome

AF:

0.569

Gnomad AMR exome

AF:

0.537

Gnomad ASJ exome

AF:

0.514

Gnomad EAS exome

AF:

0.580

Gnomad SAS exome

AF:

0.484

Gnomad FIN exome

AF:

0.506

Gnomad NFE exome

AF:

0.487

Gnomad OTH exome

AF:

0.514

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.491

AC:

569393

AN:

1159378

Hom.:

70136

Cov.:

AF XY:

0.490

AC XY:

278944

AN XY:

569402

show subpopulations

Gnomad4 AFR exome

AF:

0.567

Gnomad4 AMR exome

AF:

0.534

Gnomad4 ASJ exome

AF:

0.526

Gnomad4 EAS exome

AF:

0.596

Gnomad4 SAS exome

AF:

0.487

Gnomad4 FIN exome

AF:

0.490

Gnomad4 NFE exome

AF:

0.483

Gnomad4 OTH exome

AF:

0.508

GnomAD4 genome

AF:

0.655

AC:

97198

AN:

148482

Hom.:

32476

Cov.:

AF XY:

0.656

AC XY:

47269

AN XY:

72036

show subpopulations

Gnomad4 AFR

AF:

0.757

Gnomad4 AMR

AF:

0.671

Gnomad4 ASJ

AF:

0.698

Gnomad4 EAS

AF:

0.830

Gnomad4 SAS

AF:

0.653

Gnomad4 FIN

AF:

0.590

Gnomad4 NFE

AF:

0.585

Gnomad4 OTH

AF:

0.677

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

La Branchor

0.96

BranchPoint Hunter

6.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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