rs6099058

Positions:

• chr20-56254553-G-A

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 0.477 in 151,542 control chromosomes in the GnomAD database, including 18,548 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 0.48 (18548 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.56254553G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72152 AN: 151420 Hom.: 18506 Cov.: 31

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.477 AC: 72255 AN: 151542 Hom.: 18548 Cov.: 31 AF XY: 0.477 AC XY: 35300 AN XY: 73994

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.443

Alfa AF: 0.403 Hom.: 26682

Bravo AF: 0.478

Asia WGS AF: 0.427 AC: 1486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.25
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6099058; hg19: chr20-54829609;