Variant 2-84528872-A-ATT 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.400-22_400-21dupTT 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 0.24 ( 5262 hom., cov: 0)

Exomes 𝑓: 0.34 ( 16393 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:

DNAH6 (HGNC:):

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-ATT is Benign according to our data. Variant chr2-84528872-A-ATT is described in ClinVar as [Benign]. Clinvar id is 1271750.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH6	NM_001370.2 linkuse as main transcript	c.400-22_400-21dupTT		intron_variant		ENST00000389394.8	NP_001361.1	Q9C0G6-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
DNAH6	ENST00000389394.8 linkuse as main transcript	c.400-22_400-21dupTT	intron_variant	5	NM_001370.2	ENSP00000374045.3	Q9C0G6-1
DNAH6	ENST00000494025.1 linkuse as main transcript	n.229+10831_229+10832dupTT	intron_variant	1
DNAH6	ENST00000468661.1 linkuse as main transcript	n.454+3144_454+3145dupTT	intron_variant	4
DNAH6	ENST00000476689.5 linkuse as main transcript	n.536+3144_536+3145dupTT	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

36274

AN:

148274

Hom.:

5261

Cov.:

show subpopulations

Gnomad AFR

AF:

0.105

Gnomad AMI

AF:

0.415

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.165

Gnomad SAS

AF:

0.235

Gnomad FIN

AF:

0.333

Gnomad MID

AF:

0.179

Gnomad NFE

AF:

0.322

Gnomad OTH

AF:

0.230

GnomAD3 exomes

AF:

0.326

AC:

29680

AN:

91098

Hom.:

888

AF XY:

0.330

AC XY:

15950

AN XY:

48272

show subpopulations

Gnomad AFR exome

AF:

0.185

Gnomad AMR exome

AF:

0.298

Gnomad ASJ exome

AF:

0.341

Gnomad EAS exome

AF:

0.308

Gnomad SAS exome

AF:

0.317

Gnomad FIN exome

AF:

0.359

Gnomad NFE exome

AF:

0.346

Gnomad OTH exome

AF:

0.327

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.343

AC:

374217

AN:

1091380

Hom.:

16393

Cov.:

AF XY:

0.343

AC XY:

183598

AN XY:

535828

show subpopulations

Gnomad4 AFR exome

AF:

0.166

Gnomad4 AMR exome

AF:

0.294

Gnomad4 ASJ exome

AF:

0.330

Gnomad4 EAS exome

AF:

0.269

Gnomad4 SAS exome

AF:

0.312

Gnomad4 FIN exome

AF:

0.365

Gnomad4 NFE exome

AF:

0.354

Gnomad4 OTH exome

AF:

0.320

GnomAD4 genome

AF:

0.245

AC:

36284

AN:

148358

Hom.:

5262

Cov.:

AF XY:

0.243

AC XY:

17520

AN XY:

71966

show subpopulations

Gnomad4 AFR

AF:

0.105

Gnomad4 AMR

AF:

0.237

Gnomad4 ASJ

AF:

0.250

Gnomad4 EAS

AF:

0.165

Gnomad4 SAS

AF:

0.236

Gnomad4 FIN

AF:

0.333

Gnomad4 NFE

AF:

0.322

Gnomad4 OTH

AF:

0.231

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

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