chr15-92059513-C-G

Variant names:

• chr15-92059513-C-G
• rs995002
• NM_013272.4:c.647-35368C>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.647-35368C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 152,038 control chromosomes in the GnomAD database, including 24,377 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 0.55 (24377 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28
• Publications: 2 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=-0.5).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	NM_013272.4	MANE Select	c.647-35368C>G		intron	N/A	NP_037404.2
	SLCO3A1	NM_001145044.1		c.647-35368C>G		intron	N/A	NP_001138516.1
	SLCO3A1	NR_135775.2		n.574-35368C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	ENST00000318445.11	TSL:1 MANE Select	c.647-35368C>G		intron	N/A	ENSP00000320634.6
	SLCO3A1	ENST00000424469.2	TSL:1	c.647-35368C>G		intron	N/A	ENSP00000387846.2
	SLCO3A1	ENST00000555769.5	TSL:1	n.542-35368C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83964 AN: 151922 Hom.: 24360 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.553 AC: 84013 AN: 152038 Hom.: 24377 Cov.: 32 AF XY: 0.555 AC XY: 41260 AN XY: 74306

African (AFR) AF: 0.365 AC: 15128 AN: 41468

American (AMR) AF: 0.690 AC: 10546 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2360 AN: 3470

East Asian (EAS) AF: 0.597 AC: 3077 AN: 5150

South Asian (SAS) AF: 0.623 AC: 3006 AN: 4824

European-Finnish (FIN) AF: 0.587 AC: 6201 AN: 10568

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.615 AC: 41779 AN: 67966

Other (OTH) AF: 0.601 AC: 1265 AN: 2104

Alfa AF: 0.568 Hom.: 3103

Bravo AF: 0.556

Asia WGS AF: 0.606 AC: 2107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	15
DANN	Benign	0.57
PhyloP100		2.3
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: rs995002; hg19: chr15-92602743;