15-91917464-A-G

Variant names:

• chr15-91917464-A-G
• rs4294800
• NM_013272.4:c.646+1006A>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.646+1006A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,124 control chromosomes in the GnomAD database, including 36,358 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 0.69 (36358 hom., cov: 33)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.646+1006A>G		intron_variant	Intron 2 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.646+1006A>G		intron_variant	Intron 2 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.573+1006A>G		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.646+1006A>G		intron_variant	Intron 2 of 9	1	NM_013272.4	ENSP00000320634.6
SLCO3A1	ENST00000424469.2	c.646+1006A>G		intron_variant	Intron 2 of 10	1		ENSP00000387846.2
SLCO3A1	ENST00000555769.5	n.541+1006A>G		intron_variant	Intron 2 of 10	1
SLCO3A1	ENST00000553653.5	n.832+1006A>G		intron_variant	Intron 2 of 8	5

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104734 AN: 152006 Hom.: 36331 Cov.: 33

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.689 AC: 104805 AN: 152124 Hom.: 36358 Cov.: 33 AF XY: 0.688 AC XY: 51173 AN XY: 74352

African (AFR) AF: 0.682 AC: 28312 AN: 41494

American (AMR) AF: 0.670 AC: 10233 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2111 AN: 3468

East Asian (EAS) AF: 0.916 AC: 4737 AN: 5174

South Asian (SAS) AF: 0.779 AC: 3759 AN: 4826

European-Finnish (FIN) AF: 0.645 AC: 6814 AN: 10570

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46566 AN: 68006

Other (OTH) AF: 0.699 AC: 1476 AN: 2112

Alfa AF: 0.688 Hom.: 93621

Bravo AF: 0.693

Asia WGS AF: 0.830 AC: 2885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.44
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs4294800; hg19: chr15-92460694;