rs2227485

Variant names:

• chr12-68253933-G-A
• rs2227485

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 151,938 control chromosomes in the GnomAD database, including 21,732 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 (21732 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 57 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• 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: 0.532 AC: 80721 AN: 151820 Hom.: 21726 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.531 AC: 80754 AN: 151938 Hom.: 21732 Cov.: 32 AF XY: 0.527 AC XY: 39169 AN XY: 74266

African (AFR) AF: 0.489 AC: 20269 AN: 41420

American (AMR) AF: 0.520 AC: 7945 AN: 15278

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

East Asian (EAS) AF: 0.482 AC: 2488 AN: 5162

South Asian (SAS) AF: 0.392 AC: 1887 AN: 4814

European-Finnish (FIN) AF: 0.535 AC: 5639 AN: 10542

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39395 AN: 67938

Other (OTH) AF: 0.488 AC: 1029 AN: 2108

Alfa AF: 0.550 Hom.: 29667

Bravo AF: 0.526

Asia WGS AF: 0.405 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	13
DANN	Benign	0.68
PhyloP100		0.052
PromoterAI		-0.029	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2227485; hg19: chr12-68647713;