rs12480819

Variant names:

• chr20-17611655-A-G
• rs12480819

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 0.275 in 152,106 control chromosomes in the GnomAD database, including 6,355 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 0.28 (6355 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 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: 0.275 AC: 41837 AN: 151988 Hom.: 6339 Cov.: 33

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.275 AC: 41892 AN: 152106 Hom.: 6355 Cov.: 33 AF XY: 0.280 AC XY: 20805 AN XY: 74386

African (AFR) AF: 0.328 AC: 13608 AN: 41504

American (AMR) AF: 0.267 AC: 4075 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3470

East Asian (EAS) AF: 0.573 AC: 2956 AN: 5156

South Asian (SAS) AF: 0.447 AC: 2157 AN: 4824

European-Finnish (FIN) AF: 0.195 AC: 2061 AN: 10592

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15252 AN: 67958

Other (OTH) AF: 0.269 AC: 568 AN: 2108

Alfa AF: 0.238 Hom.: 1206

Bravo AF: 0.281

Asia WGS AF: 0.397 AC: 1379 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.81
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs12480819; hg19: chr20-17592300;