rs12151621

Variant names:

• chr2-85707376-C-A
• rs12151621

Your query was ambiguous. Multiple possible variants found:

• chr2-85707376-C-A
• chr2-85707376-C-T

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 152,128 control chromosomes in the GnomAD database, including 8,305 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 (8305 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.23
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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: 0.298 AC: 45313 AN: 152010 Hom.: 8277 Cov.: 33

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0504

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.268

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: 45395 AN: 152128 Hom.: 8305 Cov.: 33 AF XY: 0.295 AC XY: 21932 AN XY: 74354

African (AFR) AF: 0.525 AC: 21764 AN: 41462

American (AMR) AF: 0.186 AC: 2841 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3472

East Asian (EAS) AF: 0.0499 AC: 259 AN: 5186

South Asian (SAS) AF: 0.219 AC: 1055 AN: 4820

European-Finnish (FIN) AF: 0.268 AC: 2836 AN: 10568

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

European-Non Finnish (NFE) AF: 0.222 AC: 15111 AN: 68006

Other (OTH) AF: 0.244 AC: 515 AN: 2114

Alfa AF: 0.218 Hom.: 2077

Bravo AF: 0.301

Asia WGS AF: 0.190 AC: 662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.010
DANN	Benign	0.68
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs12151621; hg19: chr2-85934499;