rs3121494

Variant names:

• chr10-113669365-A-C
• rs3121494

Your query was ambiguous. Multiple possible variants found:

• chr10-113669365-A-C
• chr10-113669365-A-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 0.327 in 152,002 control chromosomes in the GnomAD database, including 8,467 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 0.33 (8467 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.415 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: 0.327 AC: 49615 AN: 151884 Hom.: 8448 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.327 AC: 49667 AN: 152002 Hom.: 8467 Cov.: 32 AF XY: 0.326 AC XY: 24243 AN XY: 74316

African (AFR) AF: 0.288 AC: 11947 AN: 41412

American (AMR) AF: 0.423 AC: 6465 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 959 AN: 3472

East Asian (EAS) AF: 0.226 AC: 1168 AN: 5176

South Asian (SAS) AF: 0.228 AC: 1095 AN: 4810

European-Finnish (FIN) AF: 0.339 AC: 3585 AN: 10568

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23433 AN: 67966

Other (OTH) AF: 0.307 AC: 649 AN: 2116

Alfa AF: 0.341 Hom.: 1485

Bravo AF: 0.337

Asia WGS AF: 0.256 AC: 893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.65
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs3121494; hg19: chr10-115429124;