chr2-218192615-A-G

Variant names:

• chr2-218192615-A-G
• rs12612347

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 0.422 in 151,886 control chromosomes in the GnomAD database, including 15,145 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 0.42 (15145 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.611 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: 0.422 AC: 64065 AN: 151768 Hom.: 15123 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.422 AC: 64119 AN: 151886 Hom.: 15145 Cov.: 31 AF XY: 0.430 AC XY: 31946 AN XY: 74218

African (AFR) AF: 0.197 AC: 8180 AN: 41442

American (AMR) AF: 0.440 AC: 6723 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1544 AN: 3460

East Asian (EAS) AF: 0.549 AC: 2828 AN: 5152

South Asian (SAS) AF: 0.629 AC: 3031 AN: 4816

European-Finnish (FIN) AF: 0.623 AC: 6558 AN: 10524

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33922 AN: 67916

Other (OTH) AF: 0.418 AC: 879 AN: 2102

Alfa AF: 0.467 Hom.: 4282

Bravo AF: 0.396

Asia WGS AF: 0.594 AC: 2064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs12612347; hg19: chr2-219057338;