rs12313946

chr12-68567804-C-Achr12-68567804-C-Gchr12-68567804-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;