rs12470529

Variant names:

• chr2-202260875-G-A
• rs12470529

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 0.103 in 147,120 control chromosomes in the GnomAD database, including 976 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 0.10 (976 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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 (NFE) allele frequency at 95% confidence interval = 0.13 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: 0.103 AC: 15145 AN: 146986 Hom.: 973 Cov.: 31

Gnomad AFR AF: 0.0355

Gnomad AMI AF: 0.0810

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0673

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.0682

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.0805

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

GnomAD4 genome AF: 0.103 AC: 15152 AN: 147120 Hom.: 976 Cov.: 31 AF XY: 0.105 AC XY: 7578 AN XY: 71860

Gnomad4 AFR AF: 0.0354

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.0673

Gnomad4 EAS AF: 0.00465

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.0795

Alfa AF: 0.113 Hom.: 137

Bravo AF: 0.0904

Asia WGS AF: 0.0440 AC: 152 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	0.91
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12470529; hg19: chr2-203125598;