Variant 6-38803320-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001206927.2(DNAH8):c.3034+9T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 1,592,854 control chromosomes in the GnomAD database, including 27,357 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1934 hom., cov: 32)

Exomes 𝑓: 0.18 ( 25423 hom. )

Consequence

DNAH8
NM_001206927.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.482

Variant links:

Genes affected

DNAH8 (HGNC:2952): (dynein axonemal heavy chain 8) The protein encoded by this gene is a heavy chain of an axonemal dynein involved in sperm and respiratory cilia motility. Axonemal dyneins generate force through hydrolysis of ATP and binding to microtubules. [provided by RefSeq, Jan 2012]

DNAH8 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=-0.87).

BP6

Variant 6-38803320-T-C is Benign according to our data. Variant chr6-38803320-T-C is described in ClinVar as [Benign]. Clinvar id is 257631.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH8	NM_001206927.2 linkuse as main transcript	c.3034+9T>C		intron_variant		ENST00000327475.11	NP_001193856.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
DNAH8	ENST00000327475.11 linkuse as main transcript	c.3034+9T>C	intron_variant	5	NM_001206927.2	ENSP00000333363	P2
DNAH8	ENST00000359357.7 linkuse as main transcript	c.2383+9T>C	intron_variant	2		ENSP00000352312	A2	Q96JB1-1
DNAH8	ENST00000449981.6 linkuse as main transcript	c.3034+9T>C	intron_variant	5		ENSP00000415331

Frequencies

GnomAD3 genomes

AF:

0.137

AC:

20878

AN:

152108

Hom.:

1935

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0349

Gnomad AMI

AF:

0.124

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.229

Gnomad EAS

AF:

0.00346

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.142

GnomAD3 exomes

AF:

0.151

AC:

36020

AN:

238588

Hom.:

3337

AF XY:

0.157

AC XY:

20179

AN XY:

128822

show subpopulations

Gnomad AFR exome

AF:

0.0300

Gnomad AMR exome

AF:

0.0959

Gnomad ASJ exome

AF:

0.230

Gnomad EAS exome

AF:

0.00372

Gnomad SAS exome

AF:

0.133

Gnomad FIN exome

AF:

0.198

Gnomad NFE exome

AF:

0.194

Gnomad OTH exome

AF:

0.183

GnomAD4 exome

AF:

0.181

AC:

260570

AN:

1440628

Hom.:

25423

Cov.:

AF XY:

0.181

AC XY:

129635

AN XY:

716320

show subpopulations

Gnomad4 AFR exome

AF:

0.0290

Gnomad4 AMR exome

AF:

0.0992

Gnomad4 ASJ exome

AF:

0.223

Gnomad4 EAS exome

AF:

0.00318

Gnomad4 SAS exome

AF:

0.133

Gnomad4 FIN exome

AF:

0.200

Gnomad4 NFE exome

AF:

0.197

Gnomad4 OTH exome

AF:

0.178

GnomAD4 genome

AF:

0.137

AC:

20874

AN:

152226

Hom.:

1934

Cov.:

AF XY:

0.136

AC XY:

10133

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.0348

Gnomad4 AMR

AF:

0.133

Gnomad4 ASJ

AF:

0.229

Gnomad4 EAS

AF:

0.00347

Gnomad4 SAS

AF:

0.122

Gnomad4 FIN

AF:

0.200

Gnomad4 NFE

AF:

0.197

Gnomad4 OTH

AF:

0.141

Alfa

AF:

0.174

Hom.:

1247

Bravo

AF:

0.125

Asia WGS

AF:

0.0680

AC:

235

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Primary ciliary dyskinesia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.18

DANN

Benign

0.29

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