12-68567804-C-A

Variant names:

• chr12-68567804-C-A
• rs12313946

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 0.367 in 151,346 control chromosomes in the GnomAD database, including 10,367 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 0.37 (10367 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 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: 0.367 AC: 55553 AN: 151238 Hom.: 10363 Cov.: 30

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.372

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.367 AC: 55573 AN: 151346 Hom.: 10367 Cov.: 30 AF XY: 0.371 AC XY: 27385 AN XY: 73912

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.355

Alfa AF: 0.373 Hom.: 24692

Bravo AF: 0.359

Asia WGS AF: 0.462 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.51
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12313946; hg19: chr12-68961584;