chr15-92061300-T-C

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

2

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]

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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=-0.98).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLCO3A1NM_013272.4 linkuse as main transcriptc.647-33581T>C intron_variant ENST00000318445.11
SLCO3A1NM_001145044.1 linkuse as main transcriptc.647-33581T>C intron_variant
SLCO3A1NR_135775.2 linkuse as main transcriptn.574-33581T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLCO3A1ENST00000318445.11 linkuse as main transcriptc.647-33581T>C intron_variant 1 NM_013272.4 P1Q9UIG8-1

Frequencies

GnomAD3 genomes
AF:
0.597
AC:
90667
AN:
151882
Hom.:
27930
Cov.:
32
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.:
32
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 providedcase-controlDepartment of Ophthalmology, College of Medicine, Hanyang University-- -

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.

Other links and lift over

dbSNP: rs12899055; hg19: chr15-92604530; API