rs2370512

Variant names:

• chr3-133933896-T-A
• rs2370512
• NM_005630.3:c.*817A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-133933896-T-A
• chr3-133933896-T-C
• chr3-133933896-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005630.3(SLCO2A1):​c.*817A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 152,100 control chromosomes in the GnomAD database, including 42,872 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 0.75 (42862 hom., cov: 32)
  • Exomes 𝑓: 0.69 (10 hom.)
• Consequence: SLCO2A1 NM_005630.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.900
• Publications: 14 publications found

Genes affected

SLCO2A1 (HGNC:10955): (solute carrier organic anion transporter family member 2A1) This gene encodes a prostaglandin transporter that is a member of the 12-membrane-spanning superfamily of transporters. The encoded protein may be involved in mediating the uptake and clearance of prostaglandins in numerous tissues. [provided by RefSeq, Dec 2011]

SLCO2A1 Gene-Disease associations (from GenCC):

• hypertrophic osteoarthropathy, primary, autosomal dominant

  Inheritance: AD Classification: DEFINITIVE Submitted by: Ambry Genetics
• hypertrophic osteoarthropathy, primary, autosomal recessive, 2

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
• chronic enteropathy associated with SLCO2A1 gene

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• pachydermoperiostosis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005630.3. 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
	SLCO2A1	NM_005630.3	MANE Select	c.*817A>T		3_prime_UTR	Exon 14 of 14	NP_005621.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO2A1	ENST00000310926.11	TSL:1 MANE Select	c.*817A>T		3_prime_UTR	Exon 14 of 14	ENSP00000311291.4

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114038 AN: 151940 Hom.: 42846 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.760

GnomAD4 exome AF: 0.690 AC: 29 AN: 42 Hom.: 10 Cov.: 0 AF XY: 0.633 AC XY: 19 AN XY: 30

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.706 AC: 24 AN: 34

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.750 AC: 114087 AN: 152058 Hom.: 42862 Cov.: 32 AF XY: 0.746 AC XY: 55460 AN XY: 74324

African (AFR) AF: 0.727 AC: 30163 AN: 41466

American (AMR) AF: 0.726 AC: 11096 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2572 AN: 3470

East Asian (EAS) AF: 0.835 AC: 4318 AN: 5174

South Asian (SAS) AF: 0.806 AC: 3883 AN: 4816

European-Finnish (FIN) AF: 0.688 AC: 7284 AN: 10582

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52285 AN: 67962

Other (OTH) AF: 0.764 AC: 1608 AN: 2106

Alfa AF: 0.768 Hom.: 24549

Bravo AF: 0.752

Asia WGS AF: 0.833 AC: 2899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.69
PhyloP100		-0.90
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: rs2370512; hg19: chr3-133652740;