rs12582821

Positions:

• chr12-107297245-T-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 0.131 in 152,082 control chromosomes in the GnomAD database, including 1,384 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 0.13 (1384 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 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: 0.131 AC: 19881 AN: 151964 Hom.: 1376 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.131 AC: 19913 AN: 152082 Hom.: 1384 Cov.: 32 AF XY: 0.134 AC XY: 9934 AN XY: 74340

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.137

Alfa AF: 0.121 Hom.: 2442

Bravo AF: 0.138

Asia WGS AF: 0.217 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12582821; hg19: chr12-107691022;