rs10505709

Variant names:

• chr8-139273861-A-G
• rs10505709

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 0.0616 in 152,278 control chromosomes in the GnomAD database, including 761 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 0.062 (761 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0615 AC: 9352 AN: 152160 Hom.: 759 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0387

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.0350

Gnomad FIN AF: 0.00970

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00265

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0616 AC: 9375 AN: 152278 Hom.: 761 Cov.: 32 AF XY: 0.0620 AC XY: 4618 AN XY: 74470

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.0390

Gnomad4 ASJ AF: 0.00519

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.0354

Gnomad4 FIN AF: 0.00970

Gnomad4 NFE AF: 0.00265

Gnomad4 OTH AF: 0.0610

Alfa AF: 0.0371 Hom.: 47

Bravo AF: 0.0694

Asia WGS AF: 0.113 AC: 390 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.1
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505709; hg19: chr8-140286104;