Variant rs9302356 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013272.4(SLCO3A1):c.*1544T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 984,790 control chromosomes in the GnomAD database, including 197,796 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 0.62 ( 29628 hom., cov: 32)

Exomes 𝑓: 0.63 ( 168168 hom. )

Consequence

SLCO3A1
NM_013272.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.330

Variant links:

Genes affected

SLCO3A1 (HGNC:10952): (solute carrier organic anion transporter family member 3A1) Predicted to enable sodium-independent organic anion transmembrane transporter activity. Involved in positive regulation of NF-kappaB transcription factor activity; positive regulation of protein phosphorylation; and prostaglandin transport. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLCO3A1 links:

ENSG00000260661 (HGNC:):

ENSG00000260661 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO3A1	NM_013272.4 link	c.*1544T>C		3_prime_UTR_variant	10/10	ENST00000318445.11	NP_037404.2	Q9UIG8-1
SLCO3A1	NM_001145044.1 link	c.1996+1681T>C		intron_variant			NP_001138516.1	Q9UIG8-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11 link	c.*1544T>C		3_prime_UTR_variant	10/10	1	NM_013272.4	ENSP00000320634.6		Q9UIG8-1

Frequencies

GnomAD3 genomes

AF:

0.619

AC:

93978

AN:

151830

Hom.:

29609

Cov.:

show subpopulations

Gnomad AFR

AF:

0.641

Gnomad AMI

AF:

0.523

Gnomad AMR

AF:

0.656

Gnomad ASJ

AF:

0.691

Gnomad EAS

AF:

0.240

Gnomad SAS

AF:

0.473

Gnomad FIN

AF:

0.583

Gnomad MID

AF:

0.744

Gnomad NFE

AF:

0.638

Gnomad OTH

AF:

0.654

GnomAD4 exome

AF:

0.634

AC:

528211

AN:

832842

Hom.:

168168

Cov.:

AF XY:

0.635

AC XY:

244175

AN XY:

384604

show subpopulations

Gnomad4 AFR exome

AF:

0.648

Gnomad4 AMR exome

AF:

0.654

Gnomad4 ASJ exome

AF:

0.692

Gnomad4 EAS exome

AF:

0.232

Gnomad4 SAS exome

AF:

0.483

Gnomad4 FIN exome

AF:

0.598

Gnomad4 NFE exome

AF:

0.639

Gnomad4 OTH exome

AF:

0.607

GnomAD4 genome

AF:

0.619

AC:

94036

AN:

151948

Hom.:

29628

Cov.:

AF XY:

0.612

AC XY:

45434

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.641

Gnomad4 AMR

AF:

0.655

Gnomad4 ASJ

AF:

0.691

Gnomad4 EAS

AF:

0.240

Gnomad4 SAS

AF:

0.475

Gnomad4 FIN

AF:

0.583

Gnomad4 NFE

AF:

0.638

Gnomad4 OTH

AF:

0.648

Alfa

AF:

0.626

Hom.:

24082

Bravo

AF:

0.633

Asia WGS

AF:

0.397

AC:

1387

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.36

DANN

Benign

0.33

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over