20-156813-T-G

Variant names:

• chr20-156813-T-G
• rs12480529

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 0.3 in 151,850 control chromosomes in the GnomAD database, including 8,042 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 0.30 (8042 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 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: 0.300 AC: 45572 AN: 151734 Hom.: 8047 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.300 AC: 45563 AN: 151850 Hom.: 8042 Cov.: 31 AF XY: 0.306 AC XY: 22710 AN XY: 74186

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.298

Alfa AF: 0.326 Hom.: 1075

Bravo AF: 0.287

Asia WGS AF: 0.399 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.0
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12480529; hg19: chr20-137454;