rs17360123

chr2-5474082-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.17 in 152,080 control chromosomes in the GnomAD database, including 2,334 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 0.17 (2334 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25863 AN: 151962 Hom.: 2330 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.170 AC: 25860 AN: 152080 Hom.: 2334 Cov.: 32 AF XY: 0.168 AC XY: 12451 AN XY: 74326

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.187

Alfa AF: 0.200 Hom.: 1448

Bravo AF: 0.168

Asia WGS AF: 0.164 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	20
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17360123; hg19: chr2-5614214;