rs6099057

Variant names:

• chr20-56254396-T-C
• rs6099057

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 0.241 in 152,054 control chromosomes in the GnomAD database, including 6,054 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 0.24 (6054 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36627 AN: 151936 Hom.: 6023 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.241 AC: 36719 AN: 152054 Hom.: 6054 Cov.: 32 AF XY: 0.244 AC XY: 18125 AN XY: 74324

African (AFR) AF: 0.469 AC: 19418 AN: 41428

American (AMR) AF: 0.205 AC: 3127 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3468

East Asian (EAS) AF: 0.269 AC: 1392 AN: 5174

South Asian (SAS) AF: 0.264 AC: 1271 AN: 4806

European-Finnish (FIN) AF: 0.202 AC: 2139 AN: 10578

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8091 AN: 68014

Other (OTH) AF: 0.202 AC: 427 AN: 2116

Alfa AF: 0.148 Hom.: 4392

Bravo AF: 0.247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.9
DANN	Benign	0.77
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs6099057; hg19: chr20-54829452;