8-79608410-G-A

Position:

• chr8-79608410-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.061 in 152,200 control chromosomes in the GnomAD database, including 494 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.061 (494 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.79608410G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9248 AN: 152082 Hom.: 488 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0743

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.0176

Gnomad FIN AF: 0.0146

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0201

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0610 AC: 9286 AN: 152200 Hom.: 494 Cov.: 33 AF XY: 0.0609 AC XY: 4535 AN XY: 74426

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.0749

Gnomad4 ASJ AF: 0.00980

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.0176

Gnomad4 FIN AF: 0.0146

Gnomad4 NFE AF: 0.0201

Gnomad4 OTH AF: 0.0442

Alfa AF: 0.0282 Hom.: 306

Bravo AF: 0.0704

Asia WGS AF: 0.117 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16906958; hg19: chr8-80520645;