Variant chr6-38875650-C-T 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_001206927.2(DNAH8):c.7680C>T(p.Val2560=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 1,611,602 control chromosomes in the GnomAD database, including 167,200 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.43 ( 15226 hom., cov: 32)

Exomes 𝑓: 0.45 ( 151974 hom. )

Consequence

DNAH8
NM_001206927.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.910

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 6-38875650-C-T is Benign according to our data. Variant chr6-38875650-C-T is described in ClinVar as [Benign]. Clinvar id is 402767.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.91 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 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.7680C>T	p.Val2560=	synonymous_variant	53/93	ENST00000327475.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH8	ENST00000327475.11 linkuse as main transcript	c.7680C>T	p.Val2560=	synonymous_variant	53/93	5	NM_001206927.2	P2
DNAH8	ENST00000359357.7 linkuse as main transcript	c.7029C>T	p.Val2343=	synonymous_variant	51/91	2		A2	Q96JB1-1
DNAH8	ENST00000449981.6 linkuse as main transcript	c.7680C>T	p.Val2560=	synonymous_variant	52/82	5

Frequencies

GnomAD3 genomes

AF:

0.434

AC:

65830

AN:

151828

Hom.:

15187

Cov.:

show subpopulations

Gnomad AFR

AF:

0.373

Gnomad AMI

AF:

0.442

Gnomad AMR

AF:

0.530

Gnomad ASJ

AF:

0.360

Gnomad EAS

AF:

0.842

Gnomad SAS

AF:

0.556

Gnomad FIN

AF:

0.372

Gnomad MID

AF:

0.395

Gnomad NFE

AF:

0.423

Gnomad OTH

AF:

0.423

GnomAD3 exomes

AF:

0.487

AC:

122409

AN:

251178

Hom.:

32294

AF XY:

0.480

AC XY:

65207

AN XY:

135760

show subpopulations

Gnomad AFR exome

AF:

0.372

Gnomad AMR exome

AF:

0.642

Gnomad ASJ exome

AF:

0.365

Gnomad EAS exome

AF:

0.847

Gnomad SAS exome

AF:

0.536

Gnomad FIN exome

AF:

0.372

Gnomad NFE exome

AF:

0.422

Gnomad OTH exome

AF:

0.431

GnomAD4 exome

AF:

0.448

AC:

654099

AN:

1459654

Hom.:

151974

Cov.:

AF XY:

0.448

AC XY:

325708

AN XY:

726256

show subpopulations

Gnomad4 AFR exome

AF:

0.362

Gnomad4 AMR exome

AF:

0.628

Gnomad4 ASJ exome

AF:

0.364

Gnomad4 EAS exome

AF:

0.821

Gnomad4 SAS exome

AF:

0.530

Gnomad4 FIN exome

AF:

0.374

Gnomad4 NFE exome

AF:

0.429

Gnomad4 OTH exome

AF:

0.456

GnomAD4 genome

AF:

0.434

AC:

65923

AN:

151948

Hom.:

15226

Cov.:

AF XY:

0.436

AC XY:

32355

AN XY:

74248

show subpopulations

Gnomad4 AFR

AF:

0.374

Gnomad4 AMR

AF:

0.531

Gnomad4 ASJ

AF:

0.360

Gnomad4 EAS

AF:

0.842

Gnomad4 SAS

AF:

0.555

Gnomad4 FIN

AF:

0.372

Gnomad4 NFE

AF:

0.423

Gnomad4 OTH

AF:

0.428

Alfa

AF:

0.416

Hom.:

5967

Bravo

AF:

0.443

Asia WGS

AF:

0.679

AC:

2361

AN:

3478

EpiCase

AF:

0.421

EpiControl

AF:

0.409

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

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 -

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

BayesDel_noAF

Benign

-0.60

CADD

Benign

0.087

DANN

Benign

0.69

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