rs7163369

Variant names:

• chr15-91990684-G-A
• rs7163369
• NM_013272.4:c.646+74226G>A

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+74226G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 151,802 control chromosomes in the GnomAD database, including 44,975 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 0.76 (44975 hom., cov: 29)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 9 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]

ENSG00000294452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.646+74226G>A		intron_variant	Intron 2 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.646+74226G>A		intron_variant	Intron 2 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.573+74226G>A		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.646+74226G>A		intron_variant	Intron 2 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115529 AN: 151694 Hom.: 44917 Cov.: 29

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.762 AC: 115642 AN: 151802 Hom.: 44975 Cov.: 29 AF XY: 0.764 AC XY: 56612 AN XY: 74116

African (AFR) AF: 0.908 AC: 37620 AN: 41432

American (AMR) AF: 0.743 AC: 11335 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2321 AN: 3470

East Asian (EAS) AF: 0.962 AC: 4969 AN: 5164

South Asian (SAS) AF: 0.793 AC: 3801 AN: 4794

European-Finnish (FIN) AF: 0.714 AC: 7444 AN: 10424

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45731 AN: 67954

Other (OTH) AF: 0.764 AC: 1610 AN: 2106

Alfa AF: 0.707 Hom.: 80474

Bravo AF: 0.773

Asia WGS AF: 0.866 AC: 3012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.059
DANN	Benign	0.76
PhyloP100		-1.9
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: rs7163369; hg19: chr15-92533914;