rs12155669

Positions:

• chr8-127767685-C-T

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 0.327 in 152,060 control chromosomes in the GnomAD database, including 9,413 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 0.33 (9413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49660 AN: 151942 Hom.: 9400 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.327 AC: 49698 AN: 152060 Hom.: 9413 Cov.: 32 AF XY: 0.324 AC XY: 24056 AN XY: 74346

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.330

Alfa AF: 0.366 Hom.: 1842

Bravo AF: 0.319

Asia WGS AF: 0.306 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12155669; hg19: chr8-128779931;