rs877869

Variant names:

• chr12-51998416-G-A
• rs877869

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 0.277 in 151,262 control chromosomes in the GnomAD database, including 6,277 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 (6277 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.47 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: 0.277 AC: 41901 AN: 151144 Hom.: 6257 Cov.: 30

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.277 AC: 41952 AN: 151262 Hom.: 6277 Cov.: 30 AF XY: 0.281 AC XY: 20706 AN XY: 73804

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.305

Alfa AF: 0.262 Hom.: 2715

Bravo AF: 0.303

Asia WGS AF: 0.324 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.054
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs877869; hg19: chr12-52392200;