rs9302356

Positions:

• chr15-92164679-T-C
• chr15-92164679-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013272.4(SLCO3A1):​c.*1544T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 984,790 control chromosomes in the GnomAD database, including 197,796 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 0.62 (29628 hom., cov: 32)
  • Exomes 𝑓: 0.63 (168168 hom.)
• Consequence: SLCO3A1 NM_013272.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO3A1	NM_013272.4	c.*1544T>C		3_prime_UTR_variant	10/10	ENST00000318445.11
SLCO3A1	NM_001145044.1	c.1996+1681T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.*1544T>C		3_prime_UTR_variant	10/10	1	NM_013272.4	P1
	ENST00000557683.1	n.418-1760A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000561674.1	n.186-7438A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93978 AN: 151830 Hom.: 29609 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.654

GnomAD4 exome AF: 0.634 AC: 528211 AN: 832842 Hom.: 168168 Cov.: 35 AF XY: 0.635 AC XY: 244175 AN XY: 384604

Gnomad4 AFR exome AF: 0.648

Gnomad4 AMR exome AF: 0.654

Gnomad4 ASJ exome AF: 0.692

Gnomad4 EAS exome AF: 0.232

Gnomad4 SAS exome AF: 0.483

Gnomad4 FIN exome AF: 0.598

Gnomad4 NFE exome AF: 0.639

Gnomad4 OTH exome AF: 0.607

GnomAD4 genome AF: 0.619 AC: 94036 AN: 151948 Hom.: 29628 Cov.: 32 AF XY: 0.612 AC XY: 45434 AN XY: 74272

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.648

Alfa AF: 0.626 Hom.: 24082

Bravo AF: 0.633

Asia WGS AF: 0.397 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.36
DANN	Benign	0.33

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: rs9302356; hg19: chr15-92707909;