rs12521153

Variant names:

• chr5-53492371-G-A
• rs12521153

Your query was ambiguous. Multiple possible variants found:

• chr5-53492371-G-A
• chr5-53492371-G-T

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 0.313 in 151,918 control chromosomes in the GnomAD database, including 7,492 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 0.31 (7492 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 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: 0.313 AC: 47539 AN: 151802 Hom.: 7487 Cov.: 31

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.313 AC: 47585 AN: 151918 Hom.: 7492 Cov.: 31 AF XY: 0.315 AC XY: 23394 AN XY: 74228

African (AFR) AF: 0.276 AC: 11430 AN: 41396

American (AMR) AF: 0.321 AC: 4897 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1139 AN: 3464

East Asian (EAS) AF: 0.332 AC: 1713 AN: 5160

South Asian (SAS) AF: 0.211 AC: 1015 AN: 4812

European-Finnish (FIN) AF: 0.370 AC: 3903 AN: 10556

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22414 AN: 67956

Other (OTH) AF: 0.327 AC: 691 AN: 2110

Alfa AF: 0.321 Hom.: 32127

Bravo AF: 0.307

Asia WGS AF: 0.245 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.22
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs12521153; hg19: chr5-52788201;