rs12613304

Variant names:

• chr2-58340157-G-A
• rs12613304

Your query was ambiguous. Multiple possible variants found:

• chr2-58340157-G-A
• chr2-58340157-G-C
• chr2-58340157-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 0.171 in 152,070 control chromosomes in the GnomAD database, including 2,402 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 0.17 (2402 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 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: 0.171 AC: 25941 AN: 151950 Hom.: 2403 Cov.: 32

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.171 AC: 25951 AN: 152070 Hom.: 2402 Cov.: 32 AF XY: 0.172 AC XY: 12772 AN XY: 74316

African (AFR) AF: 0.0945 AC: 3919 AN: 41478

American (AMR) AF: 0.208 AC: 3173 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3466

East Asian (EAS) AF: 0.311 AC: 1606 AN: 5166

South Asian (SAS) AF: 0.252 AC: 1218 AN: 4824

European-Finnish (FIN) AF: 0.178 AC: 1883 AN: 10572

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12863 AN: 67978

Other (OTH) AF: 0.206 AC: 433 AN: 2102

Alfa AF: 0.112 Hom.: 212

Bravo AF: 0.172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.085
DANN	Benign	0.35
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs12613304; hg19: chr2-58567292; COSMIC: COSV107164879;