Variant 15-92061300-T-C 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.647-33581T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 151,998 control chromosomes in the GnomAD database, including 27,953 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.60 ( 27953 hom., cov: 32)

Consequence

SLCO3A1
NM_013272.4 intron

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -0.558

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
SLCO3A1	NM_013272.4 linkuse as main transcript	c.647-33581T>C	intron_variant	ENST00000318445.11
SLCO3A1	NM_001145044.1 linkuse as main transcript	c.647-33581T>C	intron_variant
SLCO3A1	NR_135775.2 linkuse as main transcript	n.574-33581T>C	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO3A1	ENST00000318445.11 linkuse as main transcript	c.647-33581T>C		intron_variant		1	NM_013272.4	P1	Q9UIG8-1

Frequencies

GnomAD3 genomes

AF:

0.597

AC:

90667

AN:

151882

Hom.:

27930

Cov.:

show subpopulations

Gnomad AFR

AF:

0.432

Gnomad AMI

AF:

0.510

Gnomad AMR

AF:

0.747

Gnomad ASJ

AF:

0.695

Gnomad EAS

AF:

0.614

Gnomad SAS

AF:

0.633

Gnomad FIN

AF:

0.613

Gnomad MID

AF:

0.668

Gnomad NFE

AF:

0.651

Gnomad OTH

AF:

0.643

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.597

AC:

90734

AN:

151998

Hom.:

27953

Cov.:

AF XY:

0.598

AC XY:

44432

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.432

Gnomad4 AMR

AF:

0.748

Gnomad4 ASJ

AF:

0.695

Gnomad4 EAS

AF:

0.615

Gnomad4 SAS

AF:

0.634

Gnomad4 FIN

AF:

0.613

Gnomad4 NFE

AF:

0.651

Gnomad4 OTH

AF:

0.645

Alfa

AF:

0.655

Hom.:

31050

Bravo

AF:

0.603

Asia WGS

AF:

0.636

AC:

2211

AN:

3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Vascular endothelial growth factor (VEGF) inhibitor response

Other:1

association, no assertion criteria provided

case-control

Department of Ophthalmology, College of Medicine, Hanyang University

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

3.6

DANN

Benign

0.54

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