rs12566232

Variant names:

• chr1-151867362-A-C
• rs12566232

Your query was ambiguous. Multiple possible variants found:

• chr1-151867362-A-C
• chr1-151867362-A-G

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 0.227 in 151,686 control chromosomes in the GnomAD database, including 5,121 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 0.23 (5121 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.52 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: 0.228 AC: 34487 AN: 151566 Hom.: 5126 Cov.: 30

Gnomad AFR AF: 0.0507

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.227 AC: 34478 AN: 151686 Hom.: 5121 Cov.: 30 AF XY: 0.233 AC XY: 17262 AN XY: 74140

African (AFR) AF: 0.0506 AC: 2098 AN: 41454

American (AMR) AF: 0.215 AC: 3279 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1793 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1597 AN: 5130

South Asian (SAS) AF: 0.537 AC: 2585 AN: 4814

European-Finnish (FIN) AF: 0.261 AC: 2737 AN: 10504

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.288 AC: 19513 AN: 67790

Other (OTH) AF: 0.248 AC: 522 AN: 2102

Alfa AF: 0.271 Hom.: 8009

Bravo AF: 0.210

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.7
DANN	Benign	0.91
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs12566232; hg19: chr1-151839838; COSMIC: COSV69336492;