rs6108011

chr20-7571857-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.237

Alfa AF: 0.299 Hom.: 13846

Bravo AF: 0.263

Asia WGS AF: 0.206 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
Cadd	Benign	17
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6108011; hg19: chr20-7552504;