chr12-113021574-A-C

Variant names:

• chr12-113021574-A-C
• rs2464288

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 0.22 in 151,964 control chromosomes in the GnomAD database, including 4,168 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 0.22 (4168 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.625
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 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: 0.221 AC: 33491 AN: 151844 Hom.: 4169 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.220 AC: 33501 AN: 151964 Hom.: 4168 Cov.: 32 AF XY: 0.227 AC XY: 16837 AN XY: 74270

African (AFR) AF: 0.121 AC: 5011 AN: 41460

American (AMR) AF: 0.230 AC: 3508 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3468

East Asian (EAS) AF: 0.475 AC: 2451 AN: 5160

South Asian (SAS) AF: 0.328 AC: 1582 AN: 4820

European-Finnish (FIN) AF: 0.318 AC: 3350 AN: 10544

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16472 AN: 67942

Other (OTH) AF: 0.218 AC: 458 AN: 2102

Alfa AF: 0.193 Hom.: 1122

Bravo AF: 0.210

Asia WGS AF: 0.371 AC: 1289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.66
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs2464288; hg19: chr12-113459379;