rs17725255

Positions:

• chr20-18098487-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0236

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.117

Alfa AF: 0.120 Hom.: 2607

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17725255; hg19: chr20-18079131;