rs902774

Variant names:

• chr12-52880120-G-A
• rs902774

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 0.121 in 152,210 control chromosomes in the GnomAD database, including 1,214 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 0.12 (1214 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407
• Publications: 77 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 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: 0.120 AC: 18317 AN: 152092 Hom.: 1209 Cov.: 32

Gnomad AFR AF: 0.0821

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0149

Gnomad SAS AF: 0.0800

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.121 AC: 18345 AN: 152210 Hom.: 1214 Cov.: 32 AF XY: 0.119 AC XY: 8856 AN XY: 74420

African (AFR) AF: 0.0820 AC: 3404 AN: 41532

American (AMR) AF: 0.121 AC: 1857 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 518 AN: 3472

East Asian (EAS) AF: 0.0149 AC: 77 AN: 5172

South Asian (SAS) AF: 0.0803 AC: 387 AN: 4820

European-Finnish (FIN) AF: 0.166 AC: 1757 AN: 10596

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9903 AN: 68002

Other (OTH) AF: 0.123 AC: 259 AN: 2114

Alfa AF: 0.138 Hom.: 6684

Bravo AF: 0.116

Asia WGS AF: 0.0640 AC: 221 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	5.2
DANN	Benign	0.81
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs902774; hg19: chr12-53273904; COSMIC: COSV58448522;