rs1387760

Positions:

• chr12-91784007-C-T

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.683

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.91784007C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;