20-156813-T-G

Variant names:

• chr20-156813-T-G
• rs12480529

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 0.3 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.113 AC: 4663 AN: 41446

American (AMR) AF: 0.346 AC: 5272 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1277 AN: 3470

East Asian (EAS) AF: 0.517 AC: 2666 AN: 5156

South Asian (SAS) AF: 0.445 AC: 2141 AN: 4812

European-Finnish (FIN) AF: 0.417 AC: 4388 AN: 10518

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.355 AC: 24134 AN: 67918

Other (OTH) AF: 0.298 AC: 627 AN: 2102

Alfa AF: 0.298 Hom.: 1149

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
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs12480529; hg19: chr20-137454;