rs6702784

Variant names:

• chr1-36439119-A-C
• rs6702784
• NM_145047.5:c.113-209T>G

Variant summary

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

The NM_145047.5(OSCP1):​c.113-209T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0507 in 448,010 control chromosomes in the GnomAD database, including 723 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 0.045 (219 hom., cov: 33)
  • Exomes 𝑓: 0.054 (504 hom.)
• Consequence: OSCP1 NM_145047.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430

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]

LOC107984940 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSCP1	NM_145047.5	c.113-209T>G		intron_variant	Intron 1 of 9	ENST00000235532.9	NP_659484.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSCP1	ENST00000235532.9	c.113-209T>G		intron_variant	Intron 1 of 9	1	NM_145047.5	ENSP00000235532.5

Frequencies

GnomAD3 genomes AF: 0.0453 AC: 6896 AN: 152234 Hom.: 219 Cov.: 33

Gnomad AFR AF: 0.0136

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0526

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.0399

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0671

Gnomad OTH AF: 0.0584

GnomAD4 exome AF: 0.0535 AC: 15823 AN: 295658 Hom.: 504 AF XY: 0.0525 AC XY: 7970 AN XY: 151666

Gnomad4 AFR exome AF: 0.0116

Gnomad4 AMR exome AF: 0.0411

Gnomad4 ASJ exome AF: 0.0817

Gnomad4 EAS exome AF: 0.000125

Gnomad4 SAS exome AF: 0.0128

Gnomad4 FIN exome AF: 0.0427

Gnomad4 NFE exome AF: 0.0651

Gnomad4 OTH exome AF: 0.0525

GnomAD4 genome AF: 0.0453 AC: 6896 AN: 152352 Hom.: 219 Cov.: 33 AF XY: 0.0433 AC XY: 3227 AN XY: 74512

Gnomad4 AFR AF: 0.0136

Gnomad4 AMR AF: 0.0525

Gnomad4 ASJ AF: 0.0818

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0143

Gnomad4 FIN AF: 0.0399

Gnomad4 NFE AF: 0.0671

Gnomad4 OTH AF: 0.0573

Alfa AF: 0.0638 Hom.: 109

Bravo AF: 0.0431

Asia WGS AF: 0.00924 AC: 32 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.8
DANN	Benign	0.69

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: rs6702784; hg19: chr1-36904720;