rs12051963

Variant names:

• chr18-36095363-A-T
• rs12051963

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 0.228 in 151,982 control chromosomes in the GnomAD database, including 4,763 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 (4763 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 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: 0.228 AC: 34679 AN: 151864 Hom.: 4759 Cov.: 31

Gnomad AFR AF: 0.0791

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.228 AC: 34691 AN: 151982 Hom.: 4763 Cov.: 31 AF XY: 0.233 AC XY: 17304 AN XY: 74252

African (AFR) AF: 0.0790 AC: 3279 AN: 41486

American (AMR) AF: 0.285 AC: 4345 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 803 AN: 3468

East Asian (EAS) AF: 0.425 AC: 2190 AN: 5158

South Asian (SAS) AF: 0.324 AC: 1559 AN: 4816

European-Finnish (FIN) AF: 0.304 AC: 3205 AN: 10526

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18505 AN: 67962

Other (OTH) AF: 0.244 AC: 515 AN: 2108

Alfa AF: 0.236 Hom.: 597

Bravo AF: 0.219

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.1
DANN	Benign	0.34
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs12051963; hg19: chr18-33675326;