rs12155669

Variant names:

• chr8-127767685-C-T
• rs12155669

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.137 AC: 5704 AN: 41504

American (AMR) AF: 0.353 AC: 5396 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1427 AN: 3470

East Asian (EAS) AF: 0.225 AC: 1161 AN: 5154

South Asian (SAS) AF: 0.337 AC: 1621 AN: 4816

European-Finnish (FIN) AF: 0.373 AC: 3942 AN: 10578

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29225 AN: 67950

Other (OTH) AF: 0.330 AC: 697 AN: 2112

Alfa AF: 0.360 Hom.: 1851

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs12155669; hg19: chr8-128779931;