rs2163752

Variant names:

• chr5-148765575-C-T
• rs2163752

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.824

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;