rs17725255

Variant names:

• chr20-18098487-T-C
• rs17725255

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 0.101 in 152,136 control chromosomes in the GnomAD database, including 1,049 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 0.10 (1049 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 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: 0.101 AC: 15335 AN: 152016 Hom.: 1044 Cov.: 32

Gnomad AFR AF: 0.0237

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.101 AC: 15346 AN: 152136 Hom.: 1049 Cov.: 32 AF XY: 0.105 AC XY: 7833 AN XY: 74386

African (AFR) AF: 0.0236 AC: 982 AN: 41556

American (AMR) AF: 0.103 AC: 1567 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 372 AN: 3472

East Asian (EAS) AF: 0.220 AC: 1133 AN: 5140

South Asian (SAS) AF: 0.178 AC: 854 AN: 4810

European-Finnish (FIN) AF: 0.181 AC: 1920 AN: 10590

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8142 AN: 67972

Other (OTH) AF: 0.117 AC: 246 AN: 2106

Alfa AF: 0.114 Hom.: 3641

Bravo AF: 0.0930

Asia WGS AF: 0.220 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.8
DANN	Benign	0.73
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs17725255; hg19: chr20-18079131;