rs2286355

Variant names:

• chr15-92094963-G-A
• rs2286355
• NM_013272.4:c.729G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-92094963-G-A
• chr15-92094963-G-C
• chr15-92094963-G-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_013272.4(SLCO3A1):​c.729G>A​(p.Ala243Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 1,603,286 control chromosomes in the GnomAD database, including 109,712 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 0.31 (8431 hom., cov: 33)
  • Exomes 𝑓: 0.37 (101281 hom.)
• Consequence: SLCO3A1 NM_013272.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.83
• Publications: 22 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BP7: Synonymous conserved (PhyloP=-3.83 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.729G>A	p.Ala243Ala	synonymous_variant	Exon 3 of 10	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.729G>A	p.Ala243Ala	synonymous_variant	Exon 3 of 11		NP_001138516.1
SLCO3A1	NR_135775.2	n.656G>A		non_coding_transcript_exon_variant	Exon 3 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.729G>A	p.Ala243Ala	synonymous_variant	Exon 3 of 10	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47586 AN: 151932 Hom.: 8413 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.337

GnomAD2 exomes AF: 0.372 AC: 93546 AN: 251308 AF XY: 0.376

Gnomad AFR exome AF: 0.135

Gnomad AMR exome AF: 0.440

Gnomad ASJ exome AF: 0.492

Gnomad EAS exome AF: 0.385

Gnomad FIN exome AF: 0.318

Gnomad NFE exome AF: 0.378

Gnomad OTH exome AF: 0.380

GnomAD4 exome AF: 0.369 AC: 535611 AN: 1451236 Hom.: 101281 Cov.: 29 AF XY: 0.370 AC XY: 267702 AN XY: 722662

African (AFR) AF: 0.134 AC: 4481 AN: 33342

American (AMR) AF: 0.437 AC: 19537 AN: 44674

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 12823 AN: 26042

East Asian (EAS) AF: 0.427 AC: 16940 AN: 39636

South Asian (SAS) AF: 0.384 AC: 32993 AN: 85956

European-Finnish (FIN) AF: 0.328 AC: 17528 AN: 53376

Middle Eastern (MID) AF: 0.422 AC: 2425 AN: 5740

European-Non Finnish (NFE) AF: 0.369 AC: 406799 AN: 1102426

Other (OTH) AF: 0.368 AC: 22085 AN: 60044

GnomAD4 genome AF: 0.313 AC: 47619 AN: 152050 Hom.: 8431 Cov.: 33 AF XY: 0.316 AC XY: 23469 AN XY: 74302

African (AFR) AF: 0.139 AC: 5774 AN: 41480

American (AMR) AF: 0.401 AC: 6132 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1668 AN: 3468

East Asian (EAS) AF: 0.391 AC: 2024 AN: 5174

South Asian (SAS) AF: 0.384 AC: 1850 AN: 4812

European-Finnish (FIN) AF: 0.320 AC: 3370 AN: 10544

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25655 AN: 67978

Other (OTH) AF: 0.343 AC: 723 AN: 2110

Alfa AF: 0.358 Hom.: 44154

Bravo AF: 0.308

Asia WGS AF: 0.387 AC: 1345 AN: 3478

EpiCase AF: 0.375

EpiControl AF: 0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	1.2
DANN	Benign	0.78
PhyloP100		-3.8
Mutation Taster		=99/1	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: rs2286355; hg19: chr15-92638193; COSMIC: COSV59230273; COSMIC: COSV59230273;