rs6108011

Variant names:

• chr20-7571857-C-T
• rs6108011

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.277 in 152,010 control chromosomes in the GnomAD database, including 6,099 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 0.28 (6099 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42135 AN: 151892 Hom.: 6090 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.277 AC: 42153 AN: 152010 Hom.: 6099 Cov.: 32 AF XY: 0.278 AC XY: 20628 AN XY: 74298

African (AFR) AF: 0.211 AC: 8746 AN: 41438

American (AMR) AF: 0.238 AC: 3642 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1349 AN: 5172

South Asian (SAS) AF: 0.237 AC: 1145 AN: 4828

European-Finnish (FIN) AF: 0.381 AC: 4019 AN: 10554

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.318 AC: 21619 AN: 67962

Other (OTH) AF: 0.237 AC: 499 AN: 2108

Alfa AF: 0.297 Hom.: 27615

Bravo AF: 0.263

Asia WGS AF: 0.206 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	17
DANN	Benign	0.75
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs6108011; hg19: chr20-7552504;