rs35712557

chr13-78620615-TGA-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_024546.4(OBI1):c.639-3495_639-3494del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 455,938 control chromosomes in the GnomAD database, including 29,606 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.36 (10253 hom., cov: 0)
  • Exomes 𝑓: 0.35 (19353 hom.)
• Consequence: OBI1 NM_024546.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

OBI1 (HGNC:20308): (ORC ubiquitin ligase 1) Enables chromatin binding activity and ubiquitin-protein transferase activity. Involved in protein autoubiquitination; protein monoubiquitination; and regulation of DNA replication. Located in chromatin. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OBI1	NM_024546.4	c.639-3495_639-3494del		intron_variant		ENST00000282003.7
OBI1	XM_011535225.2	c.408-3495_408-3494del		intron_variant
OBI1	XM_024449410.2	c.408-3495_408-3494del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OBI1	ENST00000282003.7	c.639-3495_639-3494del		intron_variant		1	NM_024546.4	P1

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54897 AN: 151694 Hom.: 10238 Cov.: 0

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.316

GnomAD3 exomes AF: 0.331 AC: 44438 AN: 134108 Hom.: 7703 AF XY: 0.335 AC XY: 24432 AN XY: 73038

Gnomad AFR exome AF: 0.372

Gnomad AMR exome AF: 0.237

Gnomad ASJ exome AF: 0.230

Gnomad EAS exome AF: 0.372

Gnomad SAS exome AF: 0.352

Gnomad FIN exome AF: 0.543

Gnomad NFE exome AF: 0.350

Gnomad OTH exome AF: 0.307

GnomAD4 exome AF: 0.350 AC: 106558 AN: 304126 Hom.: 19353 AF XY: 0.350 AC XY: 60639 AN XY: 173178

Gnomad4 AFR exome AF: 0.375

Gnomad4 AMR exome AF: 0.236

Gnomad4 ASJ exome AF: 0.230

Gnomad4 EAS exome AF: 0.366

Gnomad4 SAS exome AF: 0.350

Gnomad4 FIN exome AF: 0.531

Gnomad4 NFE exome AF: 0.363

Gnomad4 OTH exome AF: 0.352

GnomAD4 genome AF: 0.362 AC: 54951 AN: 151812 Hom.: 10253 Cov.: 0 AF XY: 0.368 AC XY: 27295 AN XY: 74204

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.319

Alfa AF: 0.342 Hom.: 1631

Bravo AF: 0.343

Asia WGS AF: 0.387 AC: 1350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs35712557; hg19: chr13-79194750;