2-123533732-A-G

Variant names:

• chr2-123533732-A-G
• rs12612521

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 0.234 in 151,610 control chromosomes in the GnomAD database, including 5,106 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 0.23 (5106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 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: 0.234 AC: 35514 AN: 151496 Hom.: 5104 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.286

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.234 AC: 35540 AN: 151610 Hom.: 5106 Cov.: 32 AF XY: 0.244 AC XY: 18107 AN XY: 74098

African (AFR) AF: 0.167 AC: 6918 AN: 41454

American (AMR) AF: 0.331 AC: 5024 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1017 AN: 3468

East Asian (EAS) AF: 0.692 AC: 3541 AN: 5120

South Asian (SAS) AF: 0.406 AC: 1951 AN: 4808

European-Finnish (FIN) AF: 0.229 AC: 2415 AN: 10540

Middle Eastern (MID) AF: 0.291 AC: 82 AN: 282

European-Non Finnish (NFE) AF: 0.206 AC: 13956 AN: 67772

Other (OTH) AF: 0.261 AC: 548 AN: 2098

Alfa AF: 0.222 Hom.: 2591

Bravo AF: 0.240

Asia WGS AF: 0.487 AC: 1654 AN: 3406

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.32
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs12612521; hg19: chr2-124291308;