rs12470505

Variant names:

• chr2-219043647-T-G
• rs12470505

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 0.182 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
• Publications: 46 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.386 AC: 15975 AN: 41336

American (AMR) AF: 0.131 AC: 1993 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 380 AN: 3466

East Asian (EAS) AF: 0.145 AC: 750 AN: 5164

South Asian (SAS) AF: 0.0971 AC: 468 AN: 4820

European-Finnish (FIN) AF: 0.0827 AC: 876 AN: 10590

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0989 AC: 6717 AN: 67936

Other (OTH) AF: 0.184 AC: 388 AN: 2112

Alfa AF: 0.123 Hom.: 4995

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
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs12470505; hg19: chr2-219908369;