12-52892268-T-C

Variant names:

• chr12-52892268-T-C
• rs2131161

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 0.939 in 152,340 control chromosomes in the GnomAD database, including 67,266 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 0.94 (67266 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142958 AN: 152222 Hom.: 67209 Cov.: 34

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.961

Gnomad AMR AF: 0.946

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.939 AC: 143072 AN: 152340 Hom.: 67266 Cov.: 34 AF XY: 0.939 AC XY: 69943 AN XY: 74496

African (AFR) AF: 0.986 AC: 40995 AN: 41580

American (AMR) AF: 0.946 AC: 14477 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3063 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5174 AN: 5188

South Asian (SAS) AF: 0.914 AC: 4411 AN: 4826

European-Finnish (FIN) AF: 0.939 AC: 9972 AN: 10620

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61848 AN: 68024

Other (OTH) AF: 0.939 AC: 1986 AN: 2116

Alfa AF: 0.916 Hom.: 55620

Bravo AF: 0.945

Asia WGS AF: 0.937 AC: 3258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.78
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs2131161; hg19: chr12-53286052;