rs2153337

Variant names:

• chr1-36421732-C-G
• rs2153337
• NM_145047.5:c.819+418G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-36421732-C-G
• chr1-36421732-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145047.5(OSCP1):​c.819+418G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,094 control chromosomes in the GnomAD database, including 25,796 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 0.57 (25796 hom., cov: 33)
• Consequence: OSCP1 NM_145047.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 4 publications found

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]

ENSG00000297367 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145047.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSCP1	NM_145047.5	MANE Select	c.819+418G>C		intron	N/A	NP_659484.4
	OSCP1	NM_001330493.2		c.849+418G>C		intron	N/A	NP_001317422.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSCP1	ENST00000235532.9	TSL:1 MANE Select	c.819+418G>C		intron	N/A	ENSP00000235532.5
	OSCP1	ENST00000356637.9	TSL:5	c.849+418G>C		intron	N/A	ENSP00000349052.5
	OSCP1	ENST00000433045.6	TSL:5	c.684+418G>C		intron	N/A	ENSP00000390820.2

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87389 AN: 151972 Hom.: 25776 Cov.: 33

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.575 AC: 87453 AN: 152094 Hom.: 25796 Cov.: 33 AF XY: 0.572 AC XY: 42512 AN XY: 74340

African (AFR) AF: 0.702 AC: 29146 AN: 41508

American (AMR) AF: 0.469 AC: 7162 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1888 AN: 3472

East Asian (EAS) AF: 0.366 AC: 1891 AN: 5166

South Asian (SAS) AF: 0.646 AC: 3115 AN: 4824

European-Finnish (FIN) AF: 0.516 AC: 5443 AN: 10552

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 37017 AN: 67984

Other (OTH) AF: 0.563 AC: 1187 AN: 2108

Alfa AF: 0.435 Hom.: 1211

Bravo AF: 0.570

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.57
PhyloP100		0.20
PromoterAI		0.013	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2153337; hg19: chr1-36887333;