15-92094963-G-A

Position:

• chr15-92094963-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The ENST00000318445.11(SLCO3A1):​c.729G>A​(p.Ala243=) 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 ENST00000318445.11 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.83

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.729G>A	p.Ala243=	synonymous_variant	3/10	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.729G>A	p.Ala243=	synonymous_variant	3/11		NP_001138516.1
SLCO3A1	NR_135775.2	n.656G>A		non_coding_transcript_exon_variant	3/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.729G>A	p.Ala243=	synonymous_variant	3/10	1	NM_013272.4	ENSP00000320634	P1

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

GnomAD3 exomes AF: 0.372 AC: 93546 AN: 251308 Hom.: 18305 AF XY: 0.376 AC XY: 51094 AN XY: 135822

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 SAS exome AF: 0.389

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

Gnomad4 AFR exome AF: 0.134

Gnomad4 AMR exome AF: 0.437

Gnomad4 ASJ exome AF: 0.492

Gnomad4 EAS exome AF: 0.427

Gnomad4 SAS exome AF: 0.384

Gnomad4 FIN exome AF: 0.328

Gnomad4 NFE exome AF: 0.369

Gnomad4 OTH exome AF: 0.368

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

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.343

Alfa AF: 0.366 Hom.: 21909

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs2286355; hg19: chr15-92638193; COSMIC: COSV59230273; COSMIC: COSV59230273;