rs12151742

Positions:

• chr2-85705880-C-T

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 0.298 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0496

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.243

Alfa AF: 0.243 Hom.: 1455

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12151742; hg19: chr2-85933003;