rs12470505

Variant names:

• chr2-219043647-T-G
• rs12470505

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 0.182 in 151,900 control chromosomes in the GnomAD database, including 3,713 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 0.18 (3713 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 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: 0.182 AC: 27644 AN: 151782 Hom.: 3702 Cov.: 30

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0972

Gnomad FIN AF: 0.0827

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0989

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.182 AC: 27688 AN: 151900 Hom.: 3713 Cov.: 30 AF XY: 0.178 AC XY: 13225 AN XY: 74266

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.0971

Gnomad4 FIN AF: 0.0827

Gnomad4 NFE AF: 0.0989

Gnomad4 OTH AF: 0.184

Alfa AF: 0.110 Hom.: 1416

Bravo AF: 0.195

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12470505; hg19: chr2-219908369;