3-134031326-G-C

Variant names:

• chr3-134031326-G-C
• rs4241366
• ENST00000478662.1:n.94+20765C>G

Variant summary

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

The ENST00000478662.1(SLCO2A1):​n.94+20765C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0987 in 152,116 control chromosomes in the GnomAD database, including 900 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 0.099 (900 hom., cov: 32)
• Consequence: SLCO2A1 ENST00000478662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750
• Publications: 4 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=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO2A1	ENST00000478662.1	n.94+20765C>G		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.0986 AC: 14980 AN: 151996 Hom.: 895 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.0935

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0646

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.0987 AC: 15010 AN: 152116 Hom.: 900 Cov.: 32 AF XY: 0.102 AC XY: 7558 AN XY: 74352

African (AFR) AF: 0.139 AC: 5780 AN: 41454

American (AMR) AF: 0.0945 AC: 1446 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3470

East Asian (EAS) AF: 0.216 AC: 1116 AN: 5168

South Asian (SAS) AF: 0.0949 AC: 458 AN: 4824

European-Finnish (FIN) AF: 0.116 AC: 1228 AN: 10594

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0646 AC: 4395 AN: 68004

Other (OTH) AF: 0.0956 AC: 201 AN: 2102

Alfa AF: 0.0360 Hom.: 19

Bravo AF: 0.101

Asia WGS AF: 0.140 AC: 484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.7
DANN	Benign	0.85
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs4241366; hg19: chr3-133750170;