rs275769

Variant names:

• chr12-124636926-G-T
• rs275769

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 0.239 in 152,044 control chromosomes in the GnomAD database, including 4,945 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 0.24 (4945 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 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: 0.239 AC: 36291 AN: 151926 Hom.: 4939 Cov.: 34

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.0277

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.239 AC: 36310 AN: 152044 Hom.: 4945 Cov.: 34 AF XY: 0.239 AC XY: 17727 AN XY: 74314

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.0278

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.224

Alfa AF: 0.275 Hom.: 3846

Bravo AF: 0.224

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.62
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs275769; hg19: chr12-125121472;