rs2892291

Variant names:

• chr15-92086581-G-C
• rs2892291
• NM_013272.4:c.647-8300G>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.647-8300G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,918 control chromosomes in the GnomAD database, including 23,226 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 0.53 (23226 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.647-8300G>C		intron_variant	Intron 2 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.647-8300G>C		intron_variant	Intron 2 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.574-8300G>C		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.647-8300G>C		intron_variant	Intron 2 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80521 AN: 151800 Hom.: 23217 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.530 AC: 80561 AN: 151918 Hom.: 23226 Cov.: 32 AF XY: 0.529 AC XY: 39290 AN XY: 74252

African (AFR) AF: 0.313 AC: 12956 AN: 41394

American (AMR) AF: 0.534 AC: 8163 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2511 AN: 3468

East Asian (EAS) AF: 0.265 AC: 1362 AN: 5146

South Asian (SAS) AF: 0.506 AC: 2439 AN: 4816

European-Finnish (FIN) AF: 0.673 AC: 7095 AN: 10540

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.649 AC: 44137 AN: 67962

Other (OTH) AF: 0.578 AC: 1219 AN: 2108

Alfa AF: 0.586 Hom.: 3371

Bravo AF: 0.512

Asia WGS AF: 0.357 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.51
PhyloP100		-0.075
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: rs2892291; hg19: chr15-92629811;