12-51998416-G-A

Variant names:

• chr12-51998416-G-A
• rs877869

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 0.277 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.250 AC: 10305 AN: 41214

American (AMR) AF: 0.479 AC: 7256 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 772 AN: 3452

East Asian (EAS) AF: 0.304 AC: 1545 AN: 5084

South Asian (SAS) AF: 0.258 AC: 1240 AN: 4802

European-Finnish (FIN) AF: 0.236 AC: 2448 AN: 10358

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17432 AN: 67896

Other (OTH) AF: 0.305 AC: 643 AN: 2106

Alfa AF: 0.264 Hom.: 4025

Bravo AF: 0.303

Asia WGS AF: 0.324 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.054
DANN	Benign	0.50
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs877869; hg19: chr12-52392200;