rs12087334

Variant names:

• chr1-116344833-C-A
• rs12087334

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 0.279 in 151,972 control chromosomes in the GnomAD database, including 14,170 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 0.28 (14170 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 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: 0.279 AC: 42319 AN: 151854 Hom.: 14110 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0284

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0289

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.279 AC: 42429 AN: 151972 Hom.: 14170 Cov.: 32 AF XY: 0.271 AC XY: 20105 AN XY: 74286

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.0284

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0289

Gnomad4 NFE AF: 0.0690

Gnomad4 OTH AF: 0.213

Alfa AF: 0.123 Hom.: 3401

Bravo AF: 0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.40
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12087334; hg19: chr1-116887455;