5-152389060-C-T

Position:

• chr5-152389060-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 0.145 in 152,024 control chromosomes in the GnomAD database, including 2,078 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 0.14 (2078 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

Genes affected

(HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.152389060C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286749	ENST00000663460.1	n.216+13847C>T		intron_variant
ENSG00000286749	ENST00000663819.1	n.183+13847C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22005 AN: 151906 Hom.: 2081 Cov.: 32

Gnomad AFR AF: 0.0422

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0346

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.145 AC: 21994 AN: 152024 Hom.: 2078 Cov.: 32 AF XY: 0.145 AC XY: 10797 AN XY: 74312

Gnomad4 AFR AF: 0.0421

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.0347

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.142

Alfa AF: 0.108 Hom.: 292

Bravo AF: 0.147

Asia WGS AF: 0.0850 AC: 297 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	0.89
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515663; hg19: chr5-151768621;