12-68254149-G-A

Variant names:

• chr12-68254149-G-A
• rs2227484

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 0.155 in 152,066 control chromosomes in the GnomAD database, including 2,238 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 0.15 (2238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.224 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: 0.155 AC: 23559 AN: 151948 Hom.: 2237 Cov.: 32

Gnomad AFR AF: 0.0570

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.155 AC: 23563 AN: 152066 Hom.: 2238 Cov.: 32 AF XY: 0.152 AC XY: 11312 AN XY: 74322

African (AFR) AF: 0.0568 AC: 2358 AN: 41516

American (AMR) AF: 0.196 AC: 2991 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 872 AN: 3470

East Asian (EAS) AF: 0.0951 AC: 492 AN: 5172

South Asian (SAS) AF: 0.235 AC: 1134 AN: 4820

European-Finnish (FIN) AF: 0.121 AC: 1280 AN: 10550

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13800 AN: 67940

Other (OTH) AF: 0.196 AC: 412 AN: 2104

Alfa AF: 0.176 Hom.: 583

Bravo AF: 0.155

Asia WGS AF: 0.175 AC: 611 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.61
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2227484; hg19: chr12-68647929;