chr6-38722576-G-GT

Position:

• chr6-38722576-G-GT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001206927.2(DNAH8):​c.-34-200_-34-199insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,060 control chromosomes in the GnomAD database, including 6,851 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.30 (6851 hom., cov: 29)
• Consequence: DNAH8 NM_001206927.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.24

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 -10 ACMG points.

• BP6: Variant 6-38722576-G-GT is Benign according to our data. Variant chr6-38722576-G-GT is described in ClinVar as [Benign]. Clinvar id is 1227010.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH8	NM_001206927.2	c.-34-200_-34-199insT		intron_variant		ENST00000327475.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH8	ENST00000327475.11	c.-34-200_-34-199insT		intron_variant		5	NM_001206927.2	P2
DNAH8	ENST00000373278.8	c.-34-200_-34-199insT		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 44803 AN: 150956 Hom.: 6843 Cov.: 29

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.0601

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.297 AC: 44835 AN: 151060 Hom.: 6851 Cov.: 29 AF XY: 0.295 AC XY: 21733 AN XY: 73782

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.0603

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.292

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

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: rs780800732; hg19: chr6-38690352;