15-92061300-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.558

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]

ACMG classification

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
SLCO3A1	NM_013272.4	c.647-33581T>C		intron_variant		ENST00000318445.11
SLCO3A1	NM_001145044.1	c.647-33581T>C		intron_variant
SLCO3A1	NR_135775.2	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	c.647-33581T>C		intron_variant		1	NM_013272.4	P1

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90667 AN: 151882 Hom.: 27930 Cov.: 32

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

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

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

Other links and lift over

dbSNP: rs12899055; hg19: chr15-92604530;