rs12151742

Variant names:

• chr2-85705880-C-T
• rs12151742

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 0.298 in 152,100 control chromosomes in the GnomAD database, including 8,270 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 0.30 (8270 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 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: 0.297 AC: 45190 AN: 151982 Hom.: 8241 Cov.: 33

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0500

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.298 AC: 45272 AN: 152100 Hom.: 8270 Cov.: 33 AF XY: 0.294 AC XY: 21845 AN XY: 74344

African (AFR) AF: 0.525 AC: 21748 AN: 41456

American (AMR) AF: 0.185 AC: 2831 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 725 AN: 3466

East Asian (EAS) AF: 0.0496 AC: 257 AN: 5186

South Asian (SAS) AF: 0.211 AC: 1016 AN: 4826

European-Finnish (FIN) AF: 0.267 AC: 2818 AN: 10556

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15098 AN: 67996

Other (OTH) AF: 0.243 AC: 515 AN: 2116

Alfa AF: 0.237 Hom.: 2357

Bravo AF: 0.300

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.66
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs12151742; hg19: chr2-85933003;