rs6496888

Variant names:

• chr15-92023184-C-A
• rs6496888
• NM_013272.4:c.647-71697C>A

Your query was ambiguous. Multiple possible variants found:

• chr15-92023184-C-A
• chr15-92023184-C-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.647-71697C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,134 control chromosomes in the GnomAD database, including 1,454 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 0.12 (1454 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• 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]

ENSG00000304457 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.647-71697C>A		intron_variant	Intron 2 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.647-71697C>A		intron_variant	Intron 2 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.574-71697C>A		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.647-71697C>A		intron_variant	Intron 2 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17833 AN: 152016 Hom.: 1457 Cov.: 32

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0984

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.117 AC: 17838 AN: 152134 Hom.: 1454 Cov.: 32 AF XY: 0.123 AC XY: 9152 AN XY: 74374

African (AFR) AF: 0.0341 AC: 1417 AN: 41540

American (AMR) AF: 0.0983 AC: 1504 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 424 AN: 3470

East Asian (EAS) AF: 0.310 AC: 1597 AN: 5146

South Asian (SAS) AF: 0.345 AC: 1660 AN: 4812

European-Finnish (FIN) AF: 0.168 AC: 1779 AN: 10578

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.133 AC: 9071 AN: 67976

Other (OTH) AF: 0.123 AC: 260 AN: 2110

Alfa AF: 0.129 Hom.: 2426

Bravo AF: 0.103

Asia WGS AF: 0.308 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.72
PhyloP100		-0.29
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: rs6496888; hg19: chr15-92566414;