6-38722577-G-GTGTGTGT

Variant names:

• chr6-38722577-G-GTGTGTGT
• rs1491079737
• NM_001206927.2:c.-34-199_-34-198insTGTGTGT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_001206927.2(DNAH8):​c.-34-199_-34-198insTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00852 in 150,980 control chromosomes in the GnomAD database, including 14 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0085 (14 hom., cov: 30)
• Consequence: DNAH8 NM_001206927.2 intron
• Clinical Significance: Not reported in ClinVar
• 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 -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00852 (1287/150980) while in subpopulation AFR AF= 0.0289 (1186/41058). AF 95% confidence interval is 0.0275. There are 14 homozygotes in gnomad4. There are 610 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 14 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH8	NM_001206927.2	c.-34-199_-34-198insTGTGTGT		intron_variant	Intron 1 of 92	ENST00000327475.11	NP_001193856.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH8	ENST00000327475.11	c.-34-199_-34-198insTGTGTGT		intron_variant	Intron 1 of 92	5	NM_001206927.2	ENSP00000333363.7
DNAH8	ENST00000373278.8	c.-34-199_-34-198insTGTGTGT		intron_variant	Intron 1 of 4	1		ENSP00000362375.4

Frequencies

GnomAD3 genomes AF: 0.00853 AC: 1287 AN: 150864 Hom.: 14 Cov.: 30

Gnomad AFR AF: 0.0290

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00258

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000834

Gnomad FIN AF: 0.000193

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000708

Gnomad OTH AF: 0.00338

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

GnomAD4 genome AF: 0.00852 AC: 1287 AN: 150980 Hom.: 14 Cov.: 30 AF XY: 0.00828 AC XY: 610 AN XY: 73690

Gnomad4 AFR AF: 0.0289

Gnomad4 AMR AF: 0.00257

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000835

Gnomad4 FIN AF: 0.000193

Gnomad4 NFE AF: 0.000708

Gnomad4 OTH AF: 0.00334

ClinVar

Not reported in ClinVar

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;