rs2227483

Variant names:

• chr12-68254396-A-T
• rs2227483

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 0.531 in 151,154 control chromosomes in the GnomAD database, including 21,623 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 0.53 (21623 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80264 AN: 151046 Hom.: 21620 Cov.: 31

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.531 AC: 80288 AN: 151154 Hom.: 21623 Cov.: 31 AF XY: 0.527 AC XY: 38872 AN XY: 73764

African (AFR) AF: 0.489 AC: 20141 AN: 41220

American (AMR) AF: 0.520 AC: 7876 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1489 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2496 AN: 5162

South Asian (SAS) AF: 0.387 AC: 1861 AN: 4812

European-Finnish (FIN) AF: 0.534 AC: 5471 AN: 10244

Middle Eastern (MID) AF: 0.383 AC: 111 AN: 290

European-Non Finnish (NFE) AF: 0.580 AC: 39325 AN: 67802

Other (OTH) AF: 0.488 AC: 1019 AN: 2086

Alfa AF: 0.571 Hom.: 3104

Bravo AF: 0.526

Asia WGS AF: 0.401 AC: 1380 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.3
DANN	Benign	0.50
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2227483; hg19: chr12-68648176;