15-92042909-G-T

Variant names:

• chr15-92042909-G-T
• rs1400786
• NM_013272.4:c.647-51972G>T

Variant summary

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

The NM_013272.4(SLCO3A1):​c.647-51972G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 151,918 control chromosomes in the GnomAD database, including 47,235 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 0.79 (47235 hom., cov: 30)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.647-51972G>T		intron_variant	Intron 2 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.647-51972G>T		intron_variant	Intron 2 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.574-51972G>T		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.647-51972G>T		intron_variant	Intron 2 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119554 AN: 151800 Hom.: 47192 Cov.: 30

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.788 AC: 119654 AN: 151918 Hom.: 47235 Cov.: 30 AF XY: 0.787 AC XY: 58431 AN XY: 74238

African (AFR) AF: 0.759 AC: 31461 AN: 41436

American (AMR) AF: 0.885 AC: 13500 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2860 AN: 3466

East Asian (EAS) AF: 0.743 AC: 3823 AN: 5144

South Asian (SAS) AF: 0.767 AC: 3685 AN: 4802

European-Finnish (FIN) AF: 0.747 AC: 7874 AN: 10542

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53790 AN: 67954

Other (OTH) AF: 0.819 AC: 1725 AN: 2106

Alfa AF: 0.803 Hom.: 81797

Bravo AF: 0.801

Asia WGS AF: 0.779 AC: 2709 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	1.2
DANN	Benign	0.51
PhyloP100		-0.47
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: rs1400786; hg19: chr15-92586139;