5-153160794-C-T

Position:

• chr5-153160794-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 0.523 in 151,746 control chromosomes in the GnomAD database, including 21,453 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 0.52 (21453 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.153160794C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01470	ENST00000503048.1	n.91+62659G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79360 AN: 151628 Hom.: 21431 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.523 AC: 79422 AN: 151746 Hom.: 21453 Cov.: 31 AF XY: 0.530 AC XY: 39329 AN XY: 74136

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.511

Alfa AF: 0.530 Hom.: 5340

Bravo AF: 0.522

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2910032; hg19: chr5-152540354;