1-36418171-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_145047.5(OSCP1):​c.1108G>A​(p.Asp370Asn) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

OSCP1
NM_145047.5 missense

Scores

1
9
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.12
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.37351182).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OSCP1NM_145047.5 linkc.1108G>A p.Asp370Asn missense_variant Exon 10 of 10 ENST00000235532.9 NP_659484.4 Q8WVF1-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OSCP1ENST00000235532.9 linkc.1108G>A p.Asp370Asn missense_variant Exon 10 of 10 1 NM_145047.5 ENSP00000235532.5 Q8WVF1-3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Feb 12, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1108G>A (p.D370N) alteration is located in exon 10 (coding exon 10) of the OSCP1 gene. This alteration results from a G to A substitution at nucleotide position 1108, causing the aspartic acid (D) at amino acid position 370 to be replaced by an asparagine (N). 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
Benign
0.090
BayesDel_addAF
Benign
-0.15
T
BayesDel_noAF
Benign
-0.46
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.0088
.;T;T
Eigen
Uncertain
0.57
Eigen_PC
Uncertain
0.58
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.93
D;D;D
M_CAP
Benign
0.081
D
MetaRNN
Benign
0.37
T;T;T
MetaSVM
Benign
-0.62
T
MutationAssessor
Uncertain
2.7
.;M;.
PrimateAI
Uncertain
0.49
T
PROVEAN
Uncertain
-2.4
N;N;D
REVEL
Benign
0.14
Sift
Uncertain
0.0040
D;D;D
Sift4G
Uncertain
0.0080
D;D;D
Polyphen
0.97
D;P;.
Vest4
0.28
MutPred
0.16
.;Loss of phosphorylation at S377 (P = 0.1159);.;
MVP
0.53
MPC
0.41
ClinPred
0.98
D
GERP RS
5.5
Varity_R
0.25
gMVP
0.43

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-36883772; API