rs1387760

Variant names:

• chr12-91784007-C-T
• rs1387760

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.274

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1387760; hg19: chr12-92177784;