rs12471454

Variant names:

• chr2-199149760-T-C
• rs12471454

Your query was ambiguous. Multiple possible variants found:

• chr2-199149760-T-C
• chr2-199149760-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 0.529 in 138,086 control chromosomes in the GnomAD database, including 19,085 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 0.53 (19085 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 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: 0.529 AC: 72979 AN: 137994 Hom.: 19092 Cov.: 28

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.536

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.529 AC: 72983 AN: 138086 Hom.: 19085 Cov.: 28 AF XY: 0.530 AC XY: 35710 AN XY: 67332

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.521

Alfa AF: 0.511 Hom.: 3913

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12471454; hg19: chr2-200014483;