rs12909480

Variant names:

• chr15-91973239-C-T
• rs12909480
• NM_013272.4:c.646+56781C>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.646+56781C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,132 control chromosomes in the GnomAD database, including 4,165 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 0.22 (4165 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456
• Publications: 1 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.646+56781C>T		intron_variant	Intron 2 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.646+56781C>T		intron_variant	Intron 2 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.573+56781C>T		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.646+56781C>T		intron_variant	Intron 2 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33416 AN: 152014 Hom.: 4169 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.220 AC: 33411 AN: 152132 Hom.: 4165 Cov.: 32 AF XY: 0.220 AC XY: 16339 AN XY: 74372

African (AFR) AF: 0.106 AC: 4389 AN: 41520

American (AMR) AF: 0.225 AC: 3434 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 857 AN: 3468

East Asian (EAS) AF: 0.343 AC: 1764 AN: 5148

South Asian (SAS) AF: 0.305 AC: 1472 AN: 4822

European-Finnish (FIN) AF: 0.224 AC: 2366 AN: 10572

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18326 AN: 67998

Other (OTH) AF: 0.231 AC: 488 AN: 2108

Alfa AF: 0.225 Hom.: 539

Bravo AF: 0.215

Asia WGS AF: 0.277 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.28
DANN	Benign	0.69
PhyloP100		-0.46
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: rs12909480; hg19: chr15-92516469;