chr3-186832412-A-G

Variant names:

• chr3-186832412-A-G
• rs12637534

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0171 AC: 711 AN: 41568

American (AMR) AF: 0.132 AC: 2019 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 217 AN: 3470

East Asian (EAS) AF: 0.183 AC: 948 AN: 5178

South Asian (SAS) AF: 0.0666 AC: 321 AN: 4822

European-Finnish (FIN) AF: 0.252 AC: 2666 AN: 10582

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0806 AC: 5481 AN: 68016

Other (OTH) AF: 0.0757 AC: 160 AN: 2114

Alfa AF: 0.0772 Hom.: 750

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
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs12637534; hg19: chr3-186550201;