chr1-36421884-G-A

Variant names:

• chr1-36421884-G-A
• rs10493074
• NM_145047.5:c.819+266C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145047.5(OSCP1):​c.819+266C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0304 in 517,406 control chromosomes in the GnomAD database, including 1,599 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 0.072 (1232 hom., cov: 33)
  • Exomes 𝑓: 0.013 (367 hom.)
• Consequence: OSCP1 NM_145047.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 0 publications found

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]

ENSG00000297367 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSCP1	NM_145047.5	c.819+266C>T		intron_variant	Intron 7 of 9	ENST00000235532.9	NP_659484.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSCP1	ENST00000235532.9	c.819+266C>T		intron_variant	Intron 7 of 9	1	NM_145047.5	ENSP00000235532.5

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 10980 AN: 152068 Hom.: 1226 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0337

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.000828

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00348

Gnomad OTH AF: 0.0603

GnomAD4 exome AF: 0.0129 AC: 4710 AN: 365220 Hom.: 367 AF XY: 0.0115 AC XY: 2203 AN XY: 191972

African (AFR) AF: 0.242 AC: 2627 AN: 10876

American (AMR) AF: 0.0224 AC: 370 AN: 16482

Ashkenazi Jewish (ASJ) AF: 0.0336 AC: 381 AN: 11348

East Asian (EAS) AF: 0.0000790 AC: 2 AN: 25318

South Asian (SAS) AF: 0.000924 AC: 35 AN: 37870

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 22080

Middle Eastern (MID) AF: 0.0331 AC: 53 AN: 1602

European-Non Finnish (NFE) AF: 0.00308 AC: 672 AN: 218276

Other (OTH) AF: 0.0267 AC: 570 AN: 21368

GnomAD4 genome AF: 0.0724 AC: 11013 AN: 152186 Hom.: 1232 Cov.: 33 AF XY: 0.0702 AC XY: 5221 AN XY: 74416

African (AFR) AF: 0.242 AC: 10021 AN: 41472

American (AMR) AF: 0.0337 AC: 514 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5192

South Asian (SAS) AF: 0.000829 AC: 4 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10618

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00348 AC: 237 AN: 68022

Other (OTH) AF: 0.0597 AC: 126 AN: 2110

Alfa AF: 0.0503 Hom.: 106

Bravo AF: 0.0823

Asia WGS AF: 0.0170 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.2
DANN	Benign	0.74
PhyloP100		1.3
PromoterAI		-0.031	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10493074; hg19: chr1-36887485;