20-58080304-T-G

Position:

• chr20-58080304-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 0.143 in 152,186 control chromosomes in the GnomAD database, including 1,941 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 0.14 (1941 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.58080304T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21771 AN: 152068 Hom.: 1941 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.0856

Gnomad FIN AF: 0.0885

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.143 AC: 21790 AN: 152186 Hom.: 1941 Cov.: 32 AF XY: 0.139 AC XY: 10352 AN XY: 74410

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.0151

Gnomad4 SAS AF: 0.0857

Gnomad4 FIN AF: 0.0885

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.141

Alfa AF: 0.114 Hom.: 1400

Bravo AF: 0.148

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.064
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1334109; hg19: chr20-56655360;