rs12155669

Variant names:

• chr8-127767685-C-T
• rs12155669

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;