dbSNP rs6702784: OSCP1:c.113-209T>G (chr1-36439119-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.430

Publications

14 publications found

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]

OSCP1 links:

ENSG00000297367 (HGNC:):

ENSG00000297367 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
OSCP1	NM_145047.5	MANE Select	c.113-209T>G	intron	N/A	NP_659484.4
OSCP1	NM_001330493.2		c.143-209T>G	intron	N/A	NP_001317422.1	Q8WVF1-1
OSCP1	NM_206837.3		c.113-209T>G	intron	N/A	NP_996668.1	Q8WVF1-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
OSCP1	ENST00000235532.9	TSL:1 MANE Select	c.113-209T>G	intron	N/A	ENSP00000235532.5	Q8WVF1-3
OSCP1	ENST00000356637.9	TSL:5	c.143-209T>G	intron	N/A	ENSP00000349052.5	Q8WVF1-1
OSCP1	ENST00000955707.1		c.113-209T>G	intron	N/A	ENSP00000625766.1

Frequencies

GnomAD3 genomes

AF:

0.0453

AC:

6896

AN:

152234

Hom.:

219

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.0116

AC:

102

AN:

8830

American (AMR)

AF:

0.0411

AC:

412

AN:

10020

Ashkenazi Jewish (ASJ)

AF:

0.0817

AC:

840

AN:

10282

East Asian (EAS)

AF:

0.000125

AC:

AN:

24086

South Asian (SAS)

AF:

0.0128

AC:

167

AN:

13058

European-Finnish (FIN)

AF:

0.0427

AC:

952

AN:

22314

Middle Eastern (MID)

AF:

0.108

AC:

265

AN:

2460

European-Non Finnish (NFE)

AF:

0.0651

AC:

12098

AN:

185868

Other (OTH)

AF:

0.0525

AC:

984

AN:

18740

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

721

1442

2163

2884

3605

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

140

210

280

350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0453

AC:

6896

AN:

152352

Hom.:

219

Cov.:

AF XY:

0.0433

AC XY:

3227

AN XY:

74512

show subpopulations

African (AFR)

AF:

0.0136

AC:

567

AN:

41594

American (AMR)

AF:

0.0525

AC:

804

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0818

AC:

284

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5194

South Asian (SAS)

AF:

0.0143

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.0399

AC:

424

AN:

10622

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0671

AC:

4563

AN:

68018

Other (OTH)

AF:

0.0573

AC:

121

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

349

698

1048

1397

1746

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

216

288

360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0540

Hom.:

184

Bravo

AF:

0.0431

Asia WGS

AF:

0.00924

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.8

(source)

DANN

Benign

0.69

PhyloP100

0.43

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over