12-68255258-C-T

Variant names:

• chr12-68255258-C-T
• rs2227473

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 0.197 in 151,996 control chromosomes in the GnomAD database, including 3,168 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 0.20 (3168 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 24 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 (AFR) allele frequency at 95% confidence interval = 0.257 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: 0.197 AC: 29951 AN: 151878 Hom.: 3159 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.197 AC: 29986 AN: 151996 Hom.: 3168 Cov.: 32 AF XY: 0.203 AC XY: 15051 AN XY: 74294

African (AFR) AF: 0.261 AC: 10797 AN: 41428

American (AMR) AF: 0.164 AC: 2505 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 674 AN: 3468

East Asian (EAS) AF: 0.104 AC: 538 AN: 5184

South Asian (SAS) AF: 0.134 AC: 648 AN: 4818

European-Finnish (FIN) AF: 0.308 AC: 3249 AN: 10542

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.160 AC: 10885 AN: 67974

Other (OTH) AF: 0.191 AC: 404 AN: 2110

Alfa AF: 0.174 Hom.: 355

Bravo AF: 0.193

Asia WGS AF: 0.153 AC: 531 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	0.38
DANN	Benign	0.32
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2227473; hg19: chr12-68649038;