rs6083035

chr20-23200717-T-C

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 0.156 in 152,114 control chromosomes in the GnomAD database, including 2,074 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 0.16 (2074 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 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: 0.156 AC: 23680 AN: 151996 Hom.: 2071 Cov.: 32

Gnomad AFR AF: 0.0809

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.156 AC: 23693 AN: 152114 Hom.: 2074 Cov.: 32 AF XY: 0.157 AC XY: 11680 AN XY: 74360

Gnomad4 AFR AF: 0.0809

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.171

Alfa AF: 0.180 Hom.: 4431

Bravo AF: 0.150

Asia WGS AF: 0.219 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.5
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6083035; hg19: chr20-23181354;