chr12-130287208-T-C

Variant names:

• chr12-130287208-T-C
• rs1798294

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 152,176 control chromosomes in the GnomAD database, including 1,629 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 (1629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 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: 0.131 AC: 19968 AN: 152058 Hom.: 1628 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0998

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0916

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0893

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.131 AC: 19985 AN: 152176 Hom.: 1629 Cov.: 32 AF XY: 0.132 AC XY: 9789 AN XY: 74394

African (AFR) AF: 0.203 AC: 8404 AN: 41480

American (AMR) AF: 0.100 AC: 1531 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 476 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1606 AN: 5168

South Asian (SAS) AF: 0.119 AC: 572 AN: 4806

European-Finnish (FIN) AF: 0.0916 AC: 972 AN: 10606

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0892 AC: 6071 AN: 68026

Other (OTH) AF: 0.122 AC: 257 AN: 2112

Alfa AF: 0.114 Hom.: 251

Bravo AF: 0.137

Asia WGS AF: 0.195 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.5
DANN	Benign	0.51
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1798294; hg19: chr12-130771753;