rs12913189

Variant names:

• chr15-92022377-C-T
• rs12913189
• NM_013272.4:c.647-72504C>T

Variant summary

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

The NM_013272.4(SLCO3A1):​c.647-72504C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,020 control chromosomes in the GnomAD database, including 3,116 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 0.19 (3116 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 2 publications found

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]

ENSG00000304457 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.647-72504C>T		intron_variant	Intron 2 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.647-72504C>T		intron_variant	Intron 2 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.574-72504C>T		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.647-72504C>T		intron_variant	Intron 2 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29269 AN: 151902 Hom.: 3109 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.193 AC: 29306 AN: 152020 Hom.: 3116 Cov.: 32 AF XY: 0.197 AC XY: 14605 AN XY: 74306

African (AFR) AF: 0.211 AC: 8740 AN: 41432

American (AMR) AF: 0.318 AC: 4862 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 532 AN: 3466

East Asian (EAS) AF: 0.240 AC: 1235 AN: 5154

South Asian (SAS) AF: 0.215 AC: 1035 AN: 4814

European-Finnish (FIN) AF: 0.166 AC: 1762 AN: 10584

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.155 AC: 10526 AN: 67976

Other (OTH) AF: 0.185 AC: 391 AN: 2110

Alfa AF: 0.172 Hom.: 4220

Bravo AF: 0.205

Asia WGS AF: 0.225 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.44
PhyloP100		-1.1
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: rs12913189; hg19: chr15-92565607;