rs12566232

chr1-151867362-A-Cchr1-151867362-A-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 0.227 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0506

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.248

Alfa AF: 0.244 Hom.: 501

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

Splicing

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

Publications

LitVar

Other links and lift over

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