rs12621441

Variant names:

• chr2-201104217-G-A
• rs12621441

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 0.133 in 152,048 control chromosomes in the GnomAD database, including 1,592 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 0.13 (1592 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 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: 0.133 AC: 20233 AN: 151930 Hom.: 1594 Cov.: 32

Gnomad AFR AF: 0.0347

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.133 AC: 20221 AN: 152048 Hom.: 1592 Cov.: 32 AF XY: 0.133 AC XY: 9894 AN XY: 74318

Gnomad4 AFR AF: 0.0346

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.133

Alfa AF: 0.160 Hom.: 1441

Bravo AF: 0.127

Asia WGS AF: 0.134 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12621441; hg19: chr2-201968940;