15-92142548-T-C

Variant names:

• chr15-92142548-T-C
• rs2238355
• NM_013272.4:c.1513-4436T>C

Variant summary

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

The NM_013272.4(SLCO3A1):​c.1513-4436T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 152,026 control chromosomes in the GnomAD database, including 19,684 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 0.49 (19684 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 6 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.1513-4436T>C		intron_variant	Intron 7 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.1513-4436T>C		intron_variant	Intron 7 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.1440-4436T>C		intron_variant	Intron 7 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.1513-4436T>C		intron_variant	Intron 7 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74501 AN: 151908 Hom.: 19646 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.491 AC: 74586 AN: 152026 Hom.: 19684 Cov.: 32 AF XY: 0.487 AC XY: 36193 AN XY: 74304

African (AFR) AF: 0.699 AC: 28995 AN: 41460

American (AMR) AF: 0.513 AC: 7844 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1260 AN: 3470

East Asian (EAS) AF: 0.476 AC: 2454 AN: 5154

South Asian (SAS) AF: 0.348 AC: 1678 AN: 4824

European-Finnish (FIN) AF: 0.408 AC: 4303 AN: 10554

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26627 AN: 67958

Other (OTH) AF: 0.453 AC: 956 AN: 2112

Alfa AF: 0.434 Hom.: 26026

Bravo AF: 0.514

Asia WGS AF: 0.463 AC: 1613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.46
PhyloP100		-0.82
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: rs2238355; hg19: chr15-92685778;