5-158210268-C-T

Position:

• chr5-158210268-C-T

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 0.164 in 151,300 control chromosomes in the GnomAD database, including 2,153 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 0.16 (2153 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.158210268C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24832 AN: 151182 Hom.: 2144 Cov.: 30

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.164 AC: 24859 AN: 151300 Hom.: 2153 Cov.: 30 AF XY: 0.168 AC XY: 12420 AN XY: 73870

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.169

Alfa AF: 0.139 Hom.: 1992

Bravo AF: 0.159

Asia WGS AF: 0.285 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.37
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs202793; hg19: chr5-157637276;