chr12-122686671-A-G

Variant names:

• chr12-122686671-A-G
• rs2454722

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 0.289 in 152,176 control chromosomes in the GnomAD database, including 8,222 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 0.29 (8222 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43958 AN: 152056 Hom.: 8208 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.144

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.289 AC: 44005 AN: 152176 Hom.: 8222 Cov.: 32 AF XY: 0.285 AC XY: 21191 AN XY: 74420

African (AFR) AF: 0.519 AC: 21553 AN: 41494

American (AMR) AF: 0.214 AC: 3270 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 704 AN: 3468

East Asian (EAS) AF: 0.500 AC: 2592 AN: 5180

South Asian (SAS) AF: 0.138 AC: 668 AN: 4832

European-Finnish (FIN) AF: 0.162 AC: 1719 AN: 10600

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.188 AC: 12789 AN: 68002

Other (OTH) AF: 0.248 AC: 522 AN: 2106

Alfa AF: 0.209 Hom.: 2394

Bravo AF: 0.308

Asia WGS AF: 0.302 AC: 1051 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	0.66
DANN	Benign	0.67
PhyloP100		-0.68
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2454722; hg19: chr12-123171218;