Variant 2-84670393-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001370.2(DNAH6):c.6372A>G(p.Leu2124Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.956 in 1,546,402 control chromosomes in the GnomAD database, including 706,541 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.97 ( 71228 hom., cov: 33)

Exomes 𝑓: 0.95 ( 635313 hom. )

Consequence

DNAH6
NM_001370.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0500

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:

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=-0.54).

BP6

Variant 2-84670393-A-G is Benign according to our data. Variant chr2-84670393-A-G is described in ClinVar as [Benign]. Clinvar id is 402740.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.05 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 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.6372A>G	p.Leu2124Leu	synonymous_variant	39/77	ENST00000389394.8	NP_001361.1	Q9C0G6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH6	ENST00000389394.8 linkuse as main transcript	c.6372A>G	p.Leu2124Leu	synonymous_variant	39/77	5	NM_001370.2	ENSP00000374045.3		Q9C0G6-1
DNAH6	ENST00000602588.1 linkuse as main transcript	n.600A>G		non_coding_transcript_exon_variant	4/11	1

Frequencies

GnomAD3 genomes

AF:

0.967

AC:

147147

AN:

152224

Hom.:

71168

Cov.:

show subpopulations

Gnomad AFR

AF:

0.991

Gnomad AMI

AF:

0.916

Gnomad AMR

AF:

0.967

Gnomad ASJ

AF:

0.985

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.983

Gnomad FIN

AF:

0.959

Gnomad MID

AF:

0.972

Gnomad NFE

AF:

0.949

Gnomad OTH

AF:

0.969

GnomAD3 exomes

AF:

0.968

AC:

149284

AN:

154206

Hom.:

72280

AF XY:

0.969

AC XY:

78947

AN XY:

81478

show subpopulations

Gnomad AFR exome

AF:

0.993

Gnomad AMR exome

AF:

0.978

Gnomad ASJ exome

AF:

0.988

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.981

Gnomad FIN exome

AF:

0.962

Gnomad NFE exome

AF:

0.949

Gnomad OTH exome

AF:

0.964

GnomAD4 exome

AF:

0.955

AC:

1330667

AN:

1394060

Hom.:

635313

Cov.:

AF XY:

0.955

AC XY:

656941

AN XY:

687598

show subpopulations

Gnomad4 AFR exome

AF:

0.993

Gnomad4 AMR exome

AF:

0.978

Gnomad4 ASJ exome

AF:

0.989

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.983

Gnomad4 FIN exome

AF:

0.962

Gnomad4 NFE exome

AF:

0.948

Gnomad4 OTH exome

AF:

0.959

GnomAD4 genome

AF:

0.967

AC:

147266

AN:

152342

Hom.:

71228

Cov.:

AF XY:

0.968

AC XY:

72082

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.991

Gnomad4 AMR

AF:

0.967

Gnomad4 ASJ

AF:

0.985

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.983

Gnomad4 FIN

AF:

0.959

Gnomad4 NFE

AF:

0.949

Gnomad4 OTH

AF:

0.970

Alfa

AF:

0.957

Hom.:

93745

Bravo

AF:

0.969

Asia WGS

AF:

0.990

AC:

3439

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

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: MAF -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

4.8

DANN

Benign

0.77

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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