rs12634229

chr3-112657461-T-C

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 0.145 in 152,240 control chromosomes in the GnomAD database, including 2,468 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 0.14 (2468 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21983 AN: 152122 Hom.: 2457 Cov.: 33

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.0585

Gnomad FIN AF: 0.0784

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0659

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.145 AC: 22032 AN: 152240 Hom.: 2468 Cov.: 33 AF XY: 0.143 AC XY: 10674 AN XY: 74444

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.0588

Gnomad4 FIN AF: 0.0784

Gnomad4 NFE AF: 0.0659

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0797 Hom.: 1183

Bravo AF: 0.161

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12634229; hg19: chr3-112376308;