12-58517632-C-G

Variant names:

• chr12-58517632-C-G
• rs3913094

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 0.246 in 151,714 control chromosomes in the GnomAD database, including 5,697 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 0.25 (5697 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.317 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: 0.246 AC: 37242 AN: 151596 Hom.: 5688 Cov.: 31

Gnomad AFR AF: 0.0584

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.246 AC: 37261 AN: 151714 Hom.: 5697 Cov.: 31 AF XY: 0.248 AC XY: 18387 AN XY: 74126

Gnomad4 AFR AF: 0.0582

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.301

Alfa AF: 0.184 Hom.: 441

Bravo AF: 0.238

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.051
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3913094; hg19: chr12-58911415;