rs6084946

Variant names:

• chr20-569274-G-C
• rs6084946
• ENST00000784763.1:n.-157C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000784763.1(ENSG00000302168):​n.-157C>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,142 control chromosomes in the GnomAD database, including 7,998 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 (7998 hom., cov: 33)
• Consequence: ENSG00000302168 ENST00000784763.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348
• Publications: 2 publications found

Genes affected

ENSG00000302168 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784763.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302168	ENST00000784763.1		n.-157C>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46174 AN: 152024 Hom.: 7991 Cov.: 33

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.304 AC: 46204 AN: 152142 Hom.: 7998 Cov.: 33 AF XY: 0.301 AC XY: 22395 AN XY: 74374

African (AFR) AF: 0.479 AC: 19873 AN: 41494

American (AMR) AF: 0.320 AC: 4891 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3468

East Asian (EAS) AF: 0.220 AC: 1140 AN: 5174

South Asian (SAS) AF: 0.217 AC: 1047 AN: 4820

European-Finnish (FIN) AF: 0.216 AC: 2287 AN: 10594

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.218 AC: 14810 AN: 67984

Other (OTH) AF: 0.293 AC: 619 AN: 2116

Alfa AF: 0.266 Hom.: 796

Bravo AF: 0.321

Asia WGS AF: 0.242 AC: 844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.41
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs6084946; hg19: chr20-549918;