rs10505239

Variant names:

• chr8-114894998-T-C
• rs10505239

Your query was ambiguous. Multiple possible variants found:

• chr8-114894998-T-C
• chr8-114894998-T-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 0.506 in 151,776 control chromosomes in the GnomAD database, including 23,393 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 0.51 (23393 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 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: 0.506 AC: 76739 AN: 151658 Hom.: 23344 Cov.: 30

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.506 AC: 76836 AN: 151776 Hom.: 23393 Cov.: 30 AF XY: 0.504 AC XY: 37356 AN XY: 74192

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.433

Alfa AF: 0.428 Hom.: 2692

Bravo AF: 0.513

Asia WGS AF: 0.397 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505239; hg19: chr8-115907227;