rs12159200

Variant names:

• chr22-40646087-A-C
• rs12159200

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 0.229 in 152,096 control chromosomes in the GnomAD database, including 4,197 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 (4197 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630
• Publications: 7 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 = 0.342 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: 0.229 AC: 34841 AN: 151978 Hom.: 4190 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.229 AC: 34892 AN: 152096 Hom.: 4197 Cov.: 32 AF XY: 0.235 AC XY: 17488 AN XY: 74338

African (AFR) AF: 0.267 AC: 11085 AN: 41508

American (AMR) AF: 0.165 AC: 2526 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3468

East Asian (EAS) AF: 0.356 AC: 1839 AN: 5166

South Asian (SAS) AF: 0.244 AC: 1176 AN: 4826

European-Finnish (FIN) AF: 0.316 AC: 3338 AN: 10562

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13540 AN: 67972

Other (OTH) AF: 0.212 AC: 448 AN: 2112

Alfa AF: 0.211 Hom.: 11441

Bravo AF: 0.217

Asia WGS AF: 0.381 AC: 1194 AN: 3136

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.25
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs12159200; hg19: chr22-41042091;