rs12748152

Variant names:

• chr1-26811902-C-T
• rs12748152

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 0.0568 in 152,294 control chromosomes in the GnomAD database, including 319 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 0.057 (319 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616
• Publications: 79 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0773 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: 0.0568 AC: 8642 AN: 152174 Hom.: 318 Cov.: 31

Gnomad AFR AF: 0.0208

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0536

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.0229

Gnomad SAS AF: 0.0484

Gnomad FIN AF: 0.0828

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0568 AC: 8648 AN: 152294 Hom.: 319 Cov.: 31 AF XY: 0.0565 AC XY: 4211 AN XY: 74470

African (AFR) AF: 0.0209 AC: 868 AN: 41578

American (AMR) AF: 0.0534 AC: 817 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0501 AC: 174 AN: 3470

East Asian (EAS) AF: 0.0227 AC: 118 AN: 5194

South Asian (SAS) AF: 0.0487 AC: 235 AN: 4830

European-Finnish (FIN) AF: 0.0828 AC: 878 AN: 10608

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0791 AC: 5376 AN: 67998

Other (OTH) AF: 0.0539 AC: 114 AN: 2116

Alfa AF: 0.0677 Hom.: 1302

Bravo AF: 0.0526

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.83
DANN	Benign	0.41
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs12748152; hg19: chr1-27138393;