chr12-91784007-C-T

Variant names:

• chr12-91784007-C-T
• rs1387760

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.284 in 152,022 control chromosomes in the GnomAD database, including 7,215 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 0.28 (7215 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.683
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43172 AN: 151904 Hom.: 7207 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.284 AC: 43203 AN: 152022 Hom.: 7215 Cov.: 32 AF XY: 0.291 AC XY: 21596 AN XY: 74302

African (AFR) AF: 0.107 AC: 4421 AN: 41508

American (AMR) AF: 0.318 AC: 4852 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3470

East Asian (EAS) AF: 0.505 AC: 2612 AN: 5168

South Asian (SAS) AF: 0.313 AC: 1513 AN: 4830

European-Finnish (FIN) AF: 0.452 AC: 4762 AN: 10536

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23284 AN: 67948

Other (OTH) AF: 0.274 AC: 578 AN: 2108

Alfa AF: 0.313 Hom.: 1924

Bravo AF: 0.268

Asia WGS AF: 0.395 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	12
DANN	Benign	0.52
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs1387760; hg19: chr12-92177784; COSMIC: COSV107990794;