rs12621138

Variant names:

• chr2-171521535-T-A
• rs12621138

Your query was ambiguous. Multiple possible variants found:

• chr2-171521535-T-A
• chr2-171521535-T-C
• chr2-171521535-T-G

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 0.219 in 152,140 control chromosomes in the GnomAD database, including 4,288 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 0.22 (4288 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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 = 0.353 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: 0.219 AC: 33349 AN: 152022 Hom.: 4276 Cov.: 33

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.219 AC: 33391 AN: 152140 Hom.: 4288 Cov.: 33 AF XY: 0.221 AC XY: 16418 AN XY: 74378

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.188

Alfa AF: 0.0917 Hom.: 134

Bravo AF: 0.218

Asia WGS AF: 0.155 AC: 539 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	4.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12621138; hg19: chr2-172378045;