NM_013272.4:c.860A>G

Variant names:

• chr15-92104393-A-G
• rs1596104989
• NM_013272.4:c.860A>G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_013272.4(SLCO3A1):​c.860A>G​(p.Gln287Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: SLCO3A1 NM_013272.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.63
• Publications: 0 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013272.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	NM_013272.4	MANE Select	c.860A>G	p.Gln287Arg	missense	Exon 4 of 10	NP_037404.2	Q9UIG8-1
	SLCO3A1	NM_001145044.1		c.860A>G	p.Gln287Arg	missense	Exon 4 of 11	NP_001138516.1	Q9UIG8-2
	SLCO3A1	NR_135775.2		n.787A>G		non_coding_transcript_exon	Exon 4 of 11

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	ENST00000318445.11	TSL:1 MANE Select	c.860A>G	p.Gln287Arg	missense	Exon 4 of 10	ENSP00000320634.6	Q9UIG8-1
	SLCO3A1	ENST00000424469.2	TSL:1	c.860A>G	p.Gln287Arg	missense	Exon 4 of 11	ENSP00000387846.2	Q9UIG8-2
	SLCO3A1	ENST00000555769.5	TSL:1	n.755A>G		non_coding_transcript_exon	Exon 4 of 11

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.082
BayesDel_addAF	Uncertain	0.066	T
BayesDel_noAF	Benign	-0.14
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.055	T
Eigen	Benign	-0.10
Eigen_PC	Benign	0.11
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.86	D
M_CAP	Benign	0.013	T
MetaRNN	Uncertain	0.48	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.18	N
PhyloP100		6.6
PrimateAI	Uncertain	0.65	T
PROVEAN	Benign	0.62	N
REVEL	Benign	0.22
Sift	Benign	0.19	T
Sift4G	Benign	0.54	T
Polyphen		0.0090	B
Vest4		0.74
MutPred		0.44		Gain of glycosylation at P286 (P = 0.0884)
MVP		0.48
MPC		0.44
ClinPred		0.95	D
GERP RS		5.1
Varity_R		0.28
gMVP		0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.31		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.31		Position offset: 21

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1596104989; hg19: chr15-92647623;