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

Variant summary

Our verdict is Benign. Variant got -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

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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

GnomAD3 exomes

AF:

0.00494

AC:

1231

AN:

249266

Hom.:

AF XY:

0.00494

AC XY:

665

AN XY:

134740

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 SAS exome

AF:

0.000499

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

Gnomad4 AFR exome

AF:

0.000929

Gnomad4 AMR exome

AF:

0.00167

Gnomad4 ASJ exome

AF:

0.000691

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000480

Gnomad4 FIN exome

AF:

0.00159

Gnomad4 NFE exome

AF:

0.0120

Gnomad4 OTH exome

AF:

0.00719

GnomAD4 genome

AF:

0.00547

AC:

831

AN:

151986

Hom.:

Cov.:

AF XY:

0.00478

AC XY:

355

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.00232

Gnomad4 AMR

AF:

0.00210

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00125

Gnomad4 FIN

AF:

0.00114

Gnomad4 NFE

AF:

0.00985

Gnomad4 OTH

AF:

0.00379

Alfa

AF:

0.00783

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

DANN

Benign

0.58

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.013

Vest4

0.022

GERP RS

-2.8

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over