rs10505709

chr8-139273861-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;