rs12480534

Positions:

• chr20-46132846-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.264 in 152,052 control chromosomes in the GnomAD database, including 5,497 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 0.26 (5497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40178 AN: 151934 Hom.: 5495 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.264 AC: 40204 AN: 152052 Hom.: 5497 Cov.: 32 AF XY: 0.266 AC XY: 19772 AN XY: 74330

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.262

Alfa AF: 0.270 Hom.: 2140

Bravo AF: 0.269

Asia WGS AF: 0.328 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.88
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12480534; hg19: chr20-44761485;