rs12470505

Positions:

• chr2-219043647-T-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;