12-56114625-G-C

Variant names:

• chr12-56114625-G-C
• rs4759228

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 0.211 in 152,078 control chromosomes in the GnomAD database, including 3,946 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 0.21 (3946 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

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 (NFE) allele frequency at 95% confidence interval = 0.282 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: 0.211 AC: 32053 AN: 151960 Hom.: 3945 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.0716

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.211 AC: 32066 AN: 152078 Hom.: 3946 Cov.: 31 AF XY: 0.206 AC XY: 15304 AN XY: 74338

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.0714

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.234

Alfa AF: 0.244 Hom.: 592

Bravo AF: 0.205

Asia WGS AF: 0.118 AC: 415 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	9.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4759228; hg19: chr12-56508409;