rs9380791

chr6-38862634-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001206927.2(DNAH8):c.6310+176A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,016 control chromosomes in the GnomAD database, including 14,154 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.42 (14154 hom., cov: 32)
• Consequence: DNAH8 NM_001206927.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.74

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 6-38862634-A-G is Benign according to our data. Variant chr6-38862634-A-G is described in ClinVar as [Benign]. Clinvar id is 1256848.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH8	NM_001206927.2	c.6310+176A>G		intron_variant		ENST00000327475.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH8	ENST00000327475.11	c.6310+176A>G		intron_variant		5	NM_001206927.2	P2
DNAH8	ENST00000359357.7	c.5659+176A>G		intron_variant		2		A2
DNAH8	ENST00000449981.6	c.6310+176A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.421 AC: 64017 AN: 151898 Hom.: 14113 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.413

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.422 AC: 64113 AN: 152016 Hom.: 14154 Cov.: 32 AF XY: 0.421 AC XY: 31279 AN XY: 74294

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.419

Alfa AF: 0.433 Hom.: 21744

Bravo AF: 0.431

Asia WGS AF: 0.574 AC: 1997 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

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	-0.90
Cadd	Benign	0.035
Dann	Benign	0.26

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

Other links and lift over

dbSNP: rs9380791; hg19: chr6-38830410;