1-36422213-G-C

Variant names:

• chr1-36422213-G-C
• NM_145047.5:c.756C>G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_145047.5(OSCP1):​c.756C>G​(p.Ser252Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: OSCP1 NM_145047.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.0300

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSCP1	NM_145047.5	c.756C>G	p.Ser252Arg	missense_variant	Exon 7 of 10	ENST00000235532.9	NP_659484.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSCP1	ENST00000235532.9	c.756C>G	p.Ser252Arg	missense_variant	Exon 7 of 10	1	NM_145047.5	ENSP00000235532.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

May 10, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.756C>G (p.S252R) alteration is located in exon 7 (coding exon 7) of the OSCP1 gene. This alteration results from a C to G substitution at nucleotide position 756, causing the serine (S) at amino acid position 252 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.48
BayesDel_addAF	Benign	-0.069	T
BayesDel_noAF	Benign	-0.34
CADD	Benign	13
DANN	Uncertain	1.0
DEOGEN2	Benign	0.0082	.;T;T;T
Eigen	Benign	-0.35
Eigen_PC	Benign	-0.54
FATHMM_MKL	Benign	0.21	N
LIST_S2	Uncertain	0.86	D;D;D;D
M_CAP	Benign	0.046	D
MetaRNN	Uncertain	0.71	D;D;D;D
MetaSVM	Benign	-0.77	T
MutationAssessor	Uncertain	2.8	.;M;.;.
PrimateAI	Uncertain	0.55	T
PROVEAN	Benign	-1.7	N;N;N;N
REVEL	Benign	0.28
Sift	Uncertain	0.013	D;D;D;D
Sift4G	Benign	0.13	T;T;T;T
Polyphen		0.99	D;D;.;.
Vest4		0.86
MutPred		0.75		.;Gain of MoRF binding (P = 0.0115);.;.;
MVP		0.40
MPC		0.55
ClinPred		0.97	D
GERP RS		-4.0
Varity_R		0.36
gMVP		0.89

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-36887814;