rs12619019

Variant names:

• chr2-202594456-C-G
• rs12619019

Your query was ambiguous. Multiple possible variants found:

• chr2-202594456-C-G
• chr2-202594456-C-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 0.173 in 152,064 control chromosomes in the GnomAD database, including 2,752 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 (2752 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333
• Publications: 1 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 = 0.53 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: 0.173 AC: 26315 AN: 151948 Hom.: 2743 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.173 AC: 26348 AN: 152064 Hom.: 2752 Cov.: 32 AF XY: 0.177 AC XY: 13171 AN XY: 74322

African (AFR) AF: 0.112 AC: 4647 AN: 41488

American (AMR) AF: 0.220 AC: 3362 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 649 AN: 3464

East Asian (EAS) AF: 0.547 AC: 2832 AN: 5178

South Asian (SAS) AF: 0.153 AC: 736 AN: 4824

European-Finnish (FIN) AF: 0.168 AC: 1777 AN: 10556

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11788 AN: 67974

Other (OTH) AF: 0.175 AC: 370 AN: 2110

Alfa AF: 0.171 Hom.: 300

Bravo AF: 0.174

Asia WGS AF: 0.294 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.45
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs12619019; hg19: chr2-203459179;