rs10513860

Variant names:

• chr3-190701752-G-A
• rs10513860

Your query was ambiguous. Multiple possible variants found:

• chr3-190701752-G-A
• chr3-190701752-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.148 in 151,920 control chromosomes in the GnomAD database, including 3,007 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 0.15 (3007 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 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: 0.148 AC: 22431 AN: 151802 Hom.: 2988 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0213

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0575

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.148 AC: 22501 AN: 151920 Hom.: 3007 Cov.: 32 AF XY: 0.145 AC XY: 10805 AN XY: 74266

African (AFR) AF: 0.344 AC: 14239 AN: 41382

American (AMR) AF: 0.107 AC: 1631 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0542 AC: 188 AN: 3468

East Asian (EAS) AF: 0.278 AC: 1428 AN: 5140

South Asian (SAS) AF: 0.109 AC: 525 AN: 4820

European-Finnish (FIN) AF: 0.0213 AC: 226 AN: 10600

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0575 AC: 3905 AN: 67946

Other (OTH) AF: 0.113 AC: 237 AN: 2104

Alfa AF: 0.0931 Hom.: 2269

Bravo AF: 0.168

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.86
PhyloP100		0.058

Splicing

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

Other links and lift over

dbSNP: rs10513860; hg19: chr3-190419541;