rs12634229

Variant names:

• chr3-112657461-T-C
• rs12634229

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 0.145 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
• Publications: 18 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.289 AC: 11997 AN: 41504

American (AMR) AF: 0.157 AC: 2404 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3472

East Asian (EAS) AF: 0.307 AC: 1590 AN: 5180

South Asian (SAS) AF: 0.0588 AC: 284 AN: 4832

European-Finnish (FIN) AF: 0.0784 AC: 832 AN: 10610

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0659 AC: 4485 AN: 68028

Other (OTH) AF: 0.126 AC: 266 AN: 2110

Alfa AF: 0.0944 Hom.: 4065

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
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs12634229; hg19: chr3-112376308;