rs2227473

chr12-68255258-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.191

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.38
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2227473; hg19: chr12-68649038;