Genetic Variant NM_145047.5:c.516+3473G>A (chr1-36428329-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_145047.5(OSCP1):c.516+3473G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00918 in 1,610,694 control chromosomes in the GnomAD database, including 96 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0055 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0096 ( 90 hom. )

Consequence

OSCP1
NM_145047.5 intron

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.138

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_addAF=-0.769381).

BP6

Variant 1-36428329-C-T is Benign according to our data. Variant chr1-36428329-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2638672.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSCP1	NM_145047.5 link	c.516+3473G>A		intron_variant	Intron 4 of 9	ENST00000235532.9	NP_659484.4	Q8WVF1-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSCP1	ENST00000235532.9 link	c.516+3473G>A		intron_variant	Intron 4 of 9	1	NM_145047.5	ENSP00000235532.5		Q8WVF1-3

Frequencies

GnomAD3 genomes

AF:

0.00547

AC:

831

AN:

151868

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00232

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00210

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00114

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00985

Gnomad OTH

AF:

0.00383

GnomAD2 exomes

AF:

0.00494

AC:

1231

AN:

249266

AF XY:

0.00494

show subpopulations

Gnomad AFR exome

AF:

0.00179

Gnomad AMR exome

AF:

0.00153

Gnomad ASJ exome

AF:

0.000797

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00134

Gnomad NFE exome

AF:

0.00945

Gnomad OTH exome

AF:

0.00478

GnomAD4 exome

AF:

0.00957

AC:

13963

AN:

1458708

Hom.:

Cov.:

AF XY:

0.00929

AC XY:

6743

AN XY:

725526

show subpopulations

African (AFR)

AF:

0.000929

AC:

AN:

33360

American (AMR)

AF:

0.00167

AC:

AN:

44378

Ashkenazi Jewish (ASJ)

AF:

0.000691

AC:

AN:

26046

East Asian (EAS)

AF:

0.00

AC:

AN:

39636

South Asian (SAS)

AF:

0.000480

AC:

AN:

85354

European-Finnish (FIN)

AF:

0.00159

AC:

AN:

53336

Middle Eastern (MID)

AF:

0.00139

AC:

AN:

5760

European-Non Finnish (NFE)

AF:

0.0120

AC:

13273

AN:

1110584

Other (OTH)

AF:

0.00719

AC:

433

AN:

60254

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.445

Heterozygous variant carriers

780

1559

2339

3118

3898

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00547

AC:

831

AN:

151986

Hom.:

Cov.:

AF XY:

0.00478

AC XY:

355

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.00232

AC:

AN:

41438

American (AMR)

AF:

0.00210

AC:

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.00115

AC:

AN:

3470

East Asian (EAS)

AF:

0.000193

AC:

AN:

5176

South Asian (SAS)

AF:

0.00125

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.00114

AC:

AN:

10504

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00985

AC:

670

AN:

67990

Other (OTH)

AF:

0.00379

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

125

166

208

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00764

Hom.:

Bravo

AF:

0.00580

TwinsUK

AF:

0.00998

AC:

ALSPAC

AF:

0.0101

AC:

ESP6500AA

AF:

0.00295

AC:

ESP6500EA

AF:

0.00791

AC:

ExAC

AF:

0.00505

AC:

613

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Mar 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

OSCP1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.3

(source)

DANN

Benign

0.58

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.013

PhyloP100

0.14

Vest4

0.022

GERP RS

-2.8

Mutation Taster

=194/6

polymorphism

(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

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NM_145047.5:c.516+3473G>A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over