chr6-38722577-G-GTGTGT

Position:

• chr6-38722577-G-GTGTGT

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_-34-198insTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0214 in 150,962 control chromosomes in the GnomAD database, including 77 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.021 (77 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-GTGTGT is Benign according to our data. Variant chr6-38722577-G-GTGTGT is described in ClinVar as [Benign]. Clinvar id is 1230877.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0578 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0214 AC: 3231 AN: 150846 Hom.: 77 Cov.: 30

Gnomad AFR AF: 0.0599

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.00886

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.000195

Gnomad SAS AF: 0.00668

Gnomad FIN AF: 0.0177

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00571

Gnomad OTH AF: 0.0154

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

GnomAD4 genome AF: 0.0214 AC: 3234 AN: 150962 Hom.: 77 Cov.: 30 AF XY: 0.0209 AC XY: 1540 AN XY: 73676

Gnomad4 AFR AF: 0.0598

Gnomad4 AMR AF: 0.00884

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.000195

Gnomad4 SAS AF: 0.00647

Gnomad4 FIN AF: 0.0177

Gnomad4 NFE AF: 0.00571

Gnomad4 OTH AF: 0.0153

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 25, 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;