15-92112886-A-G

Variant names:

• chr15-92112886-A-G
• rs2238360
• NM_013272.4:c.1010-7579A>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.1010-7579A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,084 control chromosomes in the GnomAD database, including 12,369 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 0.39 (12369 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.1010-7579A>G		intron_variant	Intron 4 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.1010-7579A>G		intron_variant	Intron 4 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.937-7579A>G		intron_variant	Intron 4 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.1010-7579A>G		intron_variant	Intron 4 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59255 AN: 151968 Hom.: 12353 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.390 AC: 59298 AN: 152084 Hom.: 12369 Cov.: 32 AF XY: 0.393 AC XY: 29179 AN XY: 74330

African (AFR) AF: 0.229 AC: 9487 AN: 41506

American (AMR) AF: 0.469 AC: 7170 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1982 AN: 3472

East Asian (EAS) AF: 0.526 AC: 2708 AN: 5152

South Asian (SAS) AF: 0.406 AC: 1955 AN: 4816

European-Finnish (FIN) AF: 0.409 AC: 4324 AN: 10576

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30300 AN: 67954

Other (OTH) AF: 0.412 AC: 871 AN: 2116

Alfa AF: 0.430 Hom.: 24223

Bravo AF: 0.385

Asia WGS AF: 0.444 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.55
PhyloP100		0.40
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: rs2238360; hg19: chr15-92656116;