rs2163752

Positions:

• chr5-148765575-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 0.538 in 151,584 control chromosomes in the GnomAD database, including 22,433 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 0.54 (22433 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.824

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.148765575C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81411 AN: 151466 Hom.: 22402 Cov.: 30

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.538 AC: 81481 AN: 151584 Hom.: 22433 Cov.: 30 AF XY: 0.533 AC XY: 39486 AN XY: 74020

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.552

Alfa AF: 0.516 Hom.: 40506

Bravo AF: 0.546

Asia WGS AF: 0.514 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2163752; hg19: chr5-148145138;