rs12313273

Variant names:

• chr12-121625105-T-C
• rs12313273

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 0.228 in 151,890 control chromosomes in the GnomAD database, including 4,283 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 0.23 (4283 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 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: 0.228 AC: 34581 AN: 151772 Hom.: 4271 Cov.: 29

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.228 AC: 34639 AN: 151890 Hom.: 4283 Cov.: 29 AF XY: 0.231 AC XY: 17140 AN XY: 74272

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.233

Alfa AF: 0.202 Hom.: 4236

Bravo AF: 0.238

Asia WGS AF: 0.353 AC: 1228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12313273; hg19: chr12-122063010;