12-59548341-T-C

Variant names:

• chr12-59548341-T-C
• rs11533655

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 0.187 in 140,322 control chromosomes in the GnomAD database, including 6,076 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 0.19 (6076 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 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: 0.187 AC: 26285 AN: 140202 Hom.: 6071 Cov.: 25

Gnomad AFR AF: 0.0895

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.187 AC: 26305 AN: 140322 Hom.: 6076 Cov.: 25 AF XY: 0.193 AC XY: 13066 AN XY: 67828

Gnomad4 AFR AF: 0.0896

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.190

Alfa AF: 0.187 Hom.: 3864

Asia WGS AF: 0.365 AC: 1240 AN: 3398

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.55
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11533655; hg19: chr12-59942122;