NM_013272.4:c.1688+159A>G

Variant names:

• chr15-92147318-A-G
• rs732546
• NM_013272.4:c.1688+159A>G

Variant summary

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

The NM_013272.4(SLCO3A1):​c.1688+159A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,878 control chromosomes in the GnomAD database, including 9,414 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 0.35 (9414 hom., cov: 31)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.1688+159A>G		intron_variant	Intron 8 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.1688+159A>G		intron_variant	Intron 8 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.1615+159A>G		intron_variant	Intron 8 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.1688+159A>G		intron_variant	Intron 8 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53233 AN: 151758 Hom.: 9402 Cov.: 31

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.351 AC: 53260 AN: 151878 Hom.: 9414 Cov.: 31 AF XY: 0.346 AC XY: 25694 AN XY: 74240

African (AFR) AF: 0.365 AC: 15128 AN: 41420

American (AMR) AF: 0.324 AC: 4945 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1094 AN: 3470

East Asian (EAS) AF: 0.423 AC: 2180 AN: 5158

South Asian (SAS) AF: 0.285 AC: 1368 AN: 4792

European-Finnish (FIN) AF: 0.336 AC: 3552 AN: 10560

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23789 AN: 67918

Other (OTH) AF: 0.349 AC: 734 AN: 2106

Alfa AF: 0.348 Hom.: 18839

Bravo AF: 0.356

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.098
DANN	Benign	0.23
PhyloP100		-0.73
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: rs732546; hg19: chr15-92690548;