rs12185555

chr2-226694601-A-G

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 0.255 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0634

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.285

Alfa AF: 0.340 Hom.: 13463

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12185555; hg19: chr2-227559317;