rs6083035

Variant names:

• chr20-23200717-T-C
• rs6083035

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 0.156 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0809 AC: 3358 AN: 41508

American (AMR) AF: 0.120 AC: 1839 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3468

East Asian (EAS) AF: 0.310 AC: 1595 AN: 5146

South Asian (SAS) AF: 0.199 AC: 960 AN: 4820

European-Finnish (FIN) AF: 0.191 AC: 2016 AN: 10574

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12608 AN: 67994

Other (OTH) AF: 0.171 AC: 362 AN: 2112

Alfa AF: 0.176 Hom.: 9960

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
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs6083035; hg19: chr20-23181354;