dbSNP rs9380795: DNAH8:p.Lys2523Lys (chr6-38873325-G-A) – ACMG Classification: Benign (-21 pts)

Variant summary

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

The NM_001206927.2(DNAH8):c.7569G>A(p.Lys2523Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 1,611,190 control chromosomes in the GnomAD database, including 166,839 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.43 ( 15188 hom., cov: 32)

Exomes 𝑓: 0.45 ( 151651 hom. )

Consequence

DNAH8
NM_001206927.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.264

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=-0.58).

BP6

Variant 6-38873325-G-A is Benign according to our data. Variant chr6-38873325-G-A is described in ClinVar as [Benign]. Clinvar id is 402766.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.264 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH8	NM_001206927.2 link	c.7569G>A	p.Lys2523Lys	synonymous_variant	Exon 52 of 93	ENST00000327475.11	NP_001193856.1	Q96JB1Q8IU65A0A075B6F3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
DNAH8	ENST00000327475.11 link	c.7569G>A	p.Lys2523Lys	synonymous_variant	Exon 52 of 93	5	NM_001206927.2	ENSP00000333363.7	A0A075B6F3
DNAH8	ENST00000359357.7 link	c.6918G>A	p.Lys2306Lys	synonymous_variant	Exon 50 of 91	2		ENSP00000352312.3	Q96JB1-1
DNAH8	ENST00000449981.6 link	c.7569G>A	p.Lys2523Lys	synonymous_variant	Exon 51 of 82	5		ENSP00000415331.2	H0Y7V4

Frequencies

GnomAD3 genomes

AF:

0.432

AC:

65708

AN:

151936

Hom.:

15151

Cov.:

show subpopulations

Gnomad AFR

AF:

0.370

Gnomad AMI

AF:

0.444

Gnomad AMR

AF:

0.529

Gnomad ASJ

AF:

0.360

Gnomad EAS

AF:

0.841

Gnomad SAS

AF:

0.557

Gnomad FIN

AF:

0.371

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.423

Gnomad OTH

AF:

0.421

GnomAD3 exomes

AF:

0.486

AC:

120179

AN:

247394

Hom.:

31684

AF XY:

0.479

AC XY:

64010

AN XY:

133710

show subpopulations

Gnomad AFR exome

AF:

0.368

Gnomad AMR exome

AF:

0.640

Gnomad ASJ exome

AF:

0.364

Gnomad EAS exome

AF:

0.847

Gnomad SAS exome

AF:

0.533

Gnomad FIN exome

AF:

0.371

Gnomad NFE exome

AF:

0.420

Gnomad OTH exome

AF:

0.430

GnomAD4 exome

AF:

0.448

AC:

653463

AN:

1459136

Hom.:

151651

Cov.:

AF XY:

0.448

AC XY:

325236

AN XY:

725740

show subpopulations

Gnomad4 AFR exome

AF:

0.358

Gnomad4 AMR exome

AF:

0.626

Gnomad4 ASJ exome

AF:

0.363

Gnomad4 EAS exome

AF:

0.821

Gnomad4 SAS exome

AF:

0.529

Gnomad4 FIN exome

AF:

0.375

Gnomad4 NFE exome

AF:

0.429

Gnomad4 OTH exome

AF:

0.456

GnomAD4 genome

AF:

0.433

AC:

65798

AN:

152054

Hom.:

15188

Cov.:

AF XY:

0.435

AC XY:

32310

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.370

Gnomad4 AMR

AF:

0.530

Gnomad4 ASJ

AF:

0.360

Gnomad4 EAS

AF:

0.841

Gnomad4 SAS

AF:

0.556

Gnomad4 FIN

AF:

0.371

Gnomad4 NFE

AF:

0.423

Gnomad4 OTH

AF:

0.427

Alfa

AF:

0.418

Hom.:

6808

Bravo

AF:

0.441

Asia WGS

AF:

0.678

AC:

2357

AN:

3478

EpiCase

AF:

0.420

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

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

0.49

DANN

Benign

0.45

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