2-202594456-C-G

Variant names:

• chr2-202594456-C-G
• rs12619019

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.175

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12619019; hg19: chr2-203459179;