12-107297245-T-G

Variant names:

• chr12-107297245-T-G
• rs12582821

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 0.131 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
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.117 AC: 4850 AN: 41512

American (AMR) AF: 0.181 AC: 2760 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3464

East Asian (EAS) AF: 0.227 AC: 1173 AN: 5160

South Asian (SAS) AF: 0.145 AC: 696 AN: 4816

European-Finnish (FIN) AF: 0.145 AC: 1536 AN: 10574

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7633 AN: 67972

Other (OTH) AF: 0.137 AC: 289 AN: 2110

Alfa AF: 0.121 Hom.: 5004

Bravo AF: 0.138

Asia WGS AF: 0.217 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs12582821; hg19: chr12-107691022;