Variant chr6-38917234-TA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001206927.2(DNAH8):c.10141-4del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.50 ( 20282 hom., cov: 0)

Exomes 𝑓: 0.43 ( 139758 hom. )

Consequence

DNAH8
NM_001206927.2 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.492

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:

DNAH8-AS1 (HGNC:):

DNAH8-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 6-38917234-TA-T is Benign according to our data. Variant chr6-38917234-TA-T is described in ClinVar as [Benign]. Clinvar id is 257626.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-38917234-TA-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH8	NM_001206927.2 linkuse as main transcript	c.10141-4del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000327475.11
DNAH8-AS1	NR_038401.1 linkuse as main transcript	n.782+5850del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
DNAH8	ENST00000327475.11 linkuse as main transcript	c.10141-4del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	5	NM_001206927.2	P2
DNAH8	ENST00000359357.7 linkuse as main transcript	c.9490-4del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	2		A2	Q96JB1-1
DNAH8	ENST00000449981.6 linkuse as main transcript	c.10141-4del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.501

AC:

76043

AN:

151826

Hom.:

20259

Cov.:

show subpopulations

Gnomad AFR

AF:

0.688

Gnomad AMI

AF:

0.317

Gnomad AMR

AF:

0.414

Gnomad ASJ

AF:

0.420

Gnomad EAS

AF:

0.495

Gnomad SAS

AF:

0.290

Gnomad FIN

AF:

0.456

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.436

Gnomad OTH

AF:

0.469

GnomAD3 exomes

AF:

0.427

AC:

104301

AN:

244146

Hom.:

23633

AF XY:

0.418

AC XY:

55085

AN XY:

131822

show subpopulations

Gnomad AFR exome

AF:

0.690

Gnomad AMR exome

AF:

0.330

Gnomad ASJ exome

AF:

0.429

Gnomad EAS exome

AF:

0.524

Gnomad SAS exome

AF:

0.284

Gnomad FIN exome

AF:

0.451

Gnomad NFE exome

AF:

0.436

Gnomad OTH exome

AF:

0.420

GnomAD4 exome

AF:

0.434

AC:

628147

AN:

1447302

Hom.:

139758

Cov.:

AF XY:

0.430

AC XY:

309106

AN XY:

719618

show subpopulations

Gnomad4 AFR exome

AF:

0.693

Gnomad4 AMR exome

AF:

0.342

Gnomad4 ASJ exome

AF:

0.424

Gnomad4 EAS exome

AF:

0.483

Gnomad4 SAS exome

AF:

0.286

Gnomad4 FIN exome

AF:

0.449

Gnomad4 NFE exome

AF:

0.438

Gnomad4 OTH exome

AF:

0.443

GnomAD4 genome

AF:

0.501

AC:

76112

AN:

151946

Hom.:

20282

Cov.:

AF XY:

0.496

AC XY:

36811

AN XY:

74248

show subpopulations

Gnomad4 AFR

AF:

0.688

Gnomad4 AMR

AF:

0.413

Gnomad4 ASJ

AF:

0.420

Gnomad4 EAS

AF:

0.495

Gnomad4 SAS

AF:

0.291

Gnomad4 FIN

AF:

0.456

Gnomad4 NFE

AF:

0.436

Gnomad4 OTH

AF:

0.465

Alfa

AF:

0.355

Hom.:

1486

Bravo

AF:

0.507

Asia WGS

AF:

0.397

AC:

1381

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

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: Frequency -
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 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

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