6-38722577-G-GTGT

Position:

• chr6-38722577-G-GTGT

Variant summary

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

The NM_001206927.2(DNAH8):​c.-34-199_-34-198insTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 150,824 control chromosomes in the GnomAD database, including 1,682 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.14 (1682 hom., cov: 30)
• Consequence: DNAH8 NM_001206927.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.160

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 6-38722577-G-GTGT is Benign according to our data. Variant chr6-38722577-G-GTGT is described in ClinVar as [Benign]. Clinvar id is 1271210.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH8	NM_001206927.2	c.-34-199_-34-198insTGT		intron_variant		ENST00000327475.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH8	ENST00000327475.11	c.-34-199_-34-198insTGT		intron_variant		5	NM_001206927.2	P2
DNAH8	ENST00000373278.8	c.-34-199_-34-198insTGT		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21003 AN: 150708 Hom.: 1681 Cov.: 30

Gnomad AFR AF: 0.0950

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.00584

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.139 AC: 21007 AN: 150824 Hom.: 1682 Cov.: 30 AF XY: 0.139 AC XY: 10220 AN XY: 73586

Gnomad4 AFR AF: 0.0950

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.00585

Gnomad4 SAS AF: 0.0683

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.140

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

May 11, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1491079737; hg19: chr6-38690353;