rs12470529

Variant names:

• chr2-202260875-G-A
• rs12470529

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 0.103 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
• Publications: 1 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 (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

African (AFR) AF: 0.0354 AC: 1408 AN: 39740

American (AMR) AF: 0.131 AC: 1944 AN: 14842

Ashkenazi Jewish (ASJ) AF: 0.0673 AC: 228 AN: 3386

East Asian (EAS) AF: 0.00465 AC: 22 AN: 4728

South Asian (SAS) AF: 0.116 AC: 536 AN: 4622

European-Finnish (FIN) AF: 0.191 AC: 1959 AN: 10260

Middle Eastern (MID) AF: 0.0645 AC: 16 AN: 248

European-Non Finnish (NFE) AF: 0.133 AC: 8808 AN: 66406

Other (OTH) AF: 0.0795 AC: 161 AN: 2024

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12470529; hg19: chr2-203125598;