rs10493074

Positions:

• chr1-36421884-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145047.5(OSCP1):​c.819+266C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0304 in 517,406 control chromosomes in the GnomAD database, including 1,599 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 0.072 (1232 hom., cov: 33)
  • Exomes 𝑓: 0.013 (367 hom.)
• Consequence: OSCP1 NM_145047.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

Genes affected

OSCP1 (HGNC:29971): (organic solute carrier partner 1) Enables transmembrane transporter activity. Involved in xenobiotic detoxification by transmembrane export across the plasma membrane. Located in basal plasma membrane and cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSCP1	NM_145047.5	c.819+266C>T		intron_variant		ENST00000235532.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSCP1	ENST00000235532.9	c.819+266C>T		intron_variant		1	NM_145047.5	P1

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 10980 AN: 152068 Hom.: 1226 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0337

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.000828

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00348

Gnomad OTH AF: 0.0603

GnomAD4 exome AF: 0.0129 AC: 4710 AN: 365220 Hom.: 367 AF XY: 0.0115 AC XY: 2203 AN XY: 191972

Gnomad4 AFR exome AF: 0.242

Gnomad4 AMR exome AF: 0.0224

Gnomad4 ASJ exome AF: 0.0336

Gnomad4 EAS exome AF: 0.0000790

Gnomad4 SAS exome AF: 0.000924

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00308

Gnomad4 OTH exome AF: 0.0267

GnomAD4 genome AF: 0.0724 AC: 11013 AN: 152186 Hom.: 1232 Cov.: 33 AF XY: 0.0702 AC XY: 5221 AN XY: 74416

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.0337

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.000829

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00348

Gnomad4 OTH AF: 0.0597

Alfa AF: 0.0433 Hom.: 86

Bravo AF: 0.0823

Asia WGS AF: 0.0170 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.2
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs10493074; hg19: chr1-36887485;