20-58080304-T-G

Variant names:

• chr20-58080304-T-G
• rs1334109

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;