rs2920500

Variant names:

• chr3-12281914-G-A
• rs2920500

Your query was ambiguous. Multiple possible variants found:

• chr3-12281914-G-A
• chr3-12281914-G-C

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 0.499 in 151,782 control chromosomes in the GnomAD database, including 20,618 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 0.50 (20618 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.979
• Publications: 13 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 (EAS) allele frequency at 95% confidence interval = 0.902 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: 0.499 AC: 75754 AN: 151664 Hom.: 20614 Cov.: 30

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.499 AC: 75782 AN: 151782 Hom.: 20618 Cov.: 30 AF XY: 0.509 AC XY: 37725 AN XY: 74144

African (AFR) AF: 0.323 AC: 13345 AN: 41364

American (AMR) AF: 0.621 AC: 9476 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1290 AN: 3472

East Asian (EAS) AF: 0.924 AC: 4753 AN: 5146

South Asian (SAS) AF: 0.779 AC: 3746 AN: 4808

European-Finnish (FIN) AF: 0.570 AC: 5993 AN: 10508

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35670 AN: 67928

Other (OTH) AF: 0.477 AC: 1004 AN: 2106

Alfa AF: 0.525 Hom.: 60328

Bravo AF: 0.489

Asia WGS AF: 0.798 AC: 2776 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	0.12
DANN	Benign	0.40
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs2920500; hg19: chr3-12323413;