rs12185555

Variant names:

• chr2-226694601-A-G
• rs12185555

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 0.255 in 152,144 control chromosomes in the GnomAD database, including 6,215 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 0.25 (6215 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.355 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: 0.255 AC: 38773 AN: 152026 Hom.: 6213 Cov.: 32

Gnomad AFR AF: 0.0636

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.255 AC: 38781 AN: 152144 Hom.: 6215 Cov.: 32 AF XY: 0.251 AC XY: 18678 AN XY: 74390

African (AFR) AF: 0.0634 AC: 2634 AN: 41548

American (AMR) AF: 0.302 AC: 4613 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 994 AN: 3470

East Asian (EAS) AF: 0.241 AC: 1242 AN: 5156

South Asian (SAS) AF: 0.192 AC: 927 AN: 4822

European-Finnish (FIN) AF: 0.276 AC: 2919 AN: 10590

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24407 AN: 67966

Other (OTH) AF: 0.285 AC: 602 AN: 2112

Alfa AF: 0.319 Hom.: 20448

Bravo AF: 0.253

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs12185555; hg19: chr2-227559317;