rs6099058

Variant names:

• chr20-56254553-G-A
• rs6099058

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;