Variant rs78611987 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.7551T>C(p.Asp2517=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 1,613,678 control chromosomes in the GnomAD database, including 903 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 88 hom., cov: 32)

Exomes 𝑓: 0.011 ( 815 hom. )

Consequence

DNAH8
NM_001206927.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0380

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=-0.84).

BP6

Variant 6-38873307-T-C is Benign according to our data. Variant chr6-38873307-T-C is described in ClinVar as [Benign]. Clinvar id is 414422.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.038 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.138 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.7551T>C	p.Asp2517=	synonymous_variant	52/93	ENST00000327475.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH8	ENST00000327475.11 linkuse as main transcript	c.7551T>C	p.Asp2517=	synonymous_variant	52/93	5	NM_001206927.2	P2
DNAH8	ENST00000359357.7 linkuse as main transcript	c.6900T>C	p.Asp2300=	synonymous_variant	50/91	2		A2	Q96JB1-1
DNAH8	ENST00000449981.6 linkuse as main transcript	c.7551T>C	p.Asp2517=	synonymous_variant	51/82	5

Frequencies

GnomAD3 genomes

AF:

0.0110

AC:

1679

AN:

152198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00446

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00746

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.147

Gnomad SAS

AF:

0.0969

Gnomad FIN

AF:

0.000376

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00162

Gnomad OTH

AF:

0.00813

GnomAD3 exomes

AF:

0.0248

AC:

6194

AN:

249650

Hom.:

322

AF XY:

0.0277

AC XY:

3732

AN XY:

134958

show subpopulations

Gnomad AFR exome

AF:

0.00359

Gnomad AMR exome

AF:

0.0153

Gnomad ASJ exome

AF:

0.00429

Gnomad EAS exome

AF:

0.141

Gnomad SAS exome

AF:

0.0883

Gnomad FIN exome

AF:

0.000694

Gnomad NFE exome

AF:

0.00172

Gnomad OTH exome

AF:

0.0148

GnomAD4 exome

AF:

0.0112

AC:

16411

AN:

1461362

Hom.:

815

Cov.:

AF XY:

0.0136

AC XY:

9892

AN XY:

726948

show subpopulations

Gnomad4 AFR exome

AF:

0.00400

Gnomad4 AMR exome

AF:

0.0139

Gnomad4 ASJ exome

AF:

0.00448

Gnomad4 EAS exome

AF:

0.134

Gnomad4 SAS exome

AF:

0.0882

Gnomad4 FIN exome

AF:

0.000749

Gnomad4 NFE exome

AF:

0.00132

Gnomad4 OTH exome

AF:

0.0170

GnomAD4 genome

AF:

0.0110

AC:

1675

AN:

152316

Hom.:

Cov.:

AF XY:

0.0134

AC XY:

998

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.00455

Gnomad4 AMR

AF:

0.00745

Gnomad4 ASJ

AF:

0.00490

Gnomad4 EAS

AF:

0.147

Gnomad4 SAS

AF:

0.0962

Gnomad4 FIN

AF:

0.000376

Gnomad4 NFE

AF:

0.00162

Gnomad4 OTH

AF:

0.00804

Alfa

AF:

0.00325

Hom.:

Bravo

AF:

0.0102

Asia WGS

AF:

0.105

AC:

362

AN:

3476

EpiCase

AF:

0.00267

EpiControl

AF:

0.00285

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Primary ciliary dyskinesia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 25, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 04, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.0

DANN

Benign

0.39

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