12-47950255-C-T

Variant names:

• chr12-47950255-C-T
• rs1015390

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.18 in 152,110 control chromosomes in the GnomAD database, including 2,827 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 0.18 (2827 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 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: 0.180 AC: 27331 AN: 151992 Hom.: 2827 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.0680

Gnomad FIN AF: 0.0970

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.180 AC: 27335 AN: 152110 Hom.: 2827 Cov.: 32 AF XY: 0.174 AC XY: 12940 AN XY: 74366

African (AFR) AF: 0.271 AC: 11218 AN: 41464

American (AMR) AF: 0.146 AC: 2240 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 687 AN: 3472

East Asian (EAS) AF: 0.271 AC: 1402 AN: 5166

South Asian (SAS) AF: 0.0674 AC: 325 AN: 4822

European-Finnish (FIN) AF: 0.0970 AC: 1027 AN: 10588

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9934 AN: 67986

Other (OTH) AF: 0.190 AC: 401 AN: 2110

Alfa AF: 0.149 Hom.: 1628

Bravo AF: 0.190

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.59
DANN	Benign	0.62
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1015390; hg19: chr12-48344038;