15-92015004-T-G

Variant names:

• chr15-92015004-T-G
• rs2387400
• NM_013272.4:c.647-79877T>G

Variant summary

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

The NM_013272.4(SLCO3A1):​c.647-79877T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,122 control chromosomes in the GnomAD database, including 47,771 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 0.78 (47771 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.647-79877T>G		intron_variant	Intron 2 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.647-79877T>G		intron_variant	Intron 2 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.574-79877T>G		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.647-79877T>G		intron_variant	Intron 2 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119147 AN: 152004 Hom.: 47713 Cov.: 32

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.784 AC: 119264 AN: 152122 Hom.: 47771 Cov.: 32 AF XY: 0.786 AC XY: 58455 AN XY: 74344

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.762

Alfa AF: 0.706 Hom.: 50100

Bravo AF: 0.797

Asia WGS AF: 0.910 AC: 3161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.53

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: rs2387400; hg19: chr15-92558234;