chr2-5474082-G-T

Variant names:

• chr2-5474082-G-T
• rs17360123

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;