20-3089925-T-C

Variant names:

• chr20-3089925-T-C
• rs6084264

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 0.582 in 152,020 control chromosomes in the GnomAD database, including 27,324 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 0.58 (27324 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.688 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: 0.582 AC: 88434 AN: 151902 Hom.: 27314 Cov.: 31

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.582 AC: 88490 AN: 152020 Hom.: 27324 Cov.: 31 AF XY: 0.588 AC XY: 43686 AN XY: 74310

African (AFR) AF: 0.355 AC: 14702 AN: 41470

American (AMR) AF: 0.699 AC: 10673 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2072 AN: 3464

East Asian (EAS) AF: 0.677 AC: 3502 AN: 5170

South Asian (SAS) AF: 0.697 AC: 3347 AN: 4802

European-Finnish (FIN) AF: 0.677 AC: 7150 AN: 10566

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45187 AN: 67968

Other (OTH) AF: 0.591 AC: 1244 AN: 2106

Alfa AF: 0.636 Hom.: 113124

Bravo AF: 0.573

Asia WGS AF: 0.684 AC: 2376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	16
DANN	Benign	0.91
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs6084264; hg19: chr20-3070571;