rs12637534

Positions:

• chr3-186832412-A-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 0.083 in 152,240 control chromosomes in the GnomAD database, including 893 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 0.083 (893 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0830 AC: 12625 AN: 152122 Hom.: 890 Cov.: 32

Gnomad AFR AF: 0.0170

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.0667

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0806

Gnomad OTH AF: 0.0736

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

GnomAD4 genome AF: 0.0830 AC: 12639 AN: 152240 Hom.: 893 Cov.: 32 AF XY: 0.0920 AC XY: 6846 AN XY: 74430

Gnomad4 AFR AF: 0.0171

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.0625

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.0666

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.0806

Gnomad4 OTH AF: 0.0757

Alfa AF: 0.0800 Hom.: 525

Bravo AF: 0.0701

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12637534; hg19: chr3-186550201;