5-158418394-C-T

Position:

• chr5-158418394-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 0.294 in 152,008 control chromosomes in the GnomAD database, including 7,324 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 0.29 (7324 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.158418394C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44735 AN: 151888 Hom.: 7325 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.0725

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.294 AC: 44744 AN: 152008 Hom.: 7324 Cov.: 32 AF XY: 0.293 AC XY: 21759 AN XY: 74310

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.0727

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.331

Alfa AF: 0.351 Hom.: 9537

Bravo AF: 0.279

Asia WGS AF: 0.246 AC: 851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.031
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11953630; hg19: chr5-157845402;