rs6095091

chr20-48379098-C-T

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 0.302 in 151,866 control chromosomes in the GnomAD database, including 8,154 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 0.30 (8154 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 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: 0.302 AC: 45837 AN: 151748 Hom.: 8129 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.302 AC: 45924 AN: 151866 Hom.: 8154 Cov.: 31 AF XY: 0.295 AC XY: 21914 AN XY: 74226

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.258

Alfa AF: 0.252 Hom.: 5148

Bravo AF: 0.314

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.5
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6095091; hg19: chr20-47007841;