chr20-5298669-T-G

Variant names:

• chr20-5298669-T-G
• rs927102

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 0.73 in 151,626 control chromosomes in the GnomAD database, including 40,404 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 0.73 (40404 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.749 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: 0.730 AC: 110634 AN: 151506 Hom.: 40361 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.730 AC: 110727 AN: 151626 Hom.: 40404 Cov.: 33 AF XY: 0.732 AC XY: 54210 AN XY: 74086

African (AFR) AF: 0.686 AC: 28336 AN: 41292

American (AMR) AF: 0.730 AC: 11139 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2749 AN: 3470

East Asian (EAS) AF: 0.686 AC: 3532 AN: 5152

South Asian (SAS) AF: 0.769 AC: 3707 AN: 4818

European-Finnish (FIN) AF: 0.772 AC: 8106 AN: 10506

Middle Eastern (MID) AF: 0.722 AC: 208 AN: 288

European-Non Finnish (NFE) AF: 0.750 AC: 50863 AN: 67842

Other (OTH) AF: 0.735 AC: 1546 AN: 2102

Alfa AF: 0.733 Hom.: 6171

Bravo AF: 0.727

Asia WGS AF: 0.693 AC: 2410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	12
DANN	Benign	0.68
PhyloP100		-0.032

Splicing

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

Other links and lift over

dbSNP: rs927102; hg19: chr20-5279315;