rs7625035

Variant names:

• chr3-134009022-G-A
• rs7625035
• NM_005630.3:c.96+20685C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-134009022-G-A
• chr3-134009022-G-T

Variant summary

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

The NM_005630.3(SLCO2A1):​c.96+20685C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,092 control chromosomes in the GnomAD database, including 43,255 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 (43255 hom., cov: 32)
• Consequence: SLCO2A1 NM_005630.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 10 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, STRONG Submitted by: PanelApp Australia, Ambry Genetics
• hypertrophic osteoarthropathy, primary, autosomal recessive, 2

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), Genomics England PanelApp, G2P, Ambry Genetics
• inflammatory bowel disease

  Inheritance: AR Classification: STRONG Submitted by: PanelApp Australia
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.783 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO2A1	NM_005630.3	MANE Select	c.96+20685C>T		intron	N/A	NP_005621.2	Q92959

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO2A1	ENST00000310926.11	TSL:1 MANE Select	c.96+20685C>T		intron	N/A	ENSP00000311291.4	Q92959
	SLCO2A1	ENST00000464676.5	TSL:1	n.220-10236C>T		intron	N/A
	SLCO2A1	ENST00000860072.1		c.96+20685C>T		intron	N/A	ENSP00000530131.1

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114309 AN: 151974 Hom.: 43205 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.752 AC: 114416 AN: 152092 Hom.: 43255 Cov.: 32 AF XY: 0.747 AC XY: 55513 AN XY: 74342

African (AFR) AF: 0.724 AC: 30046 AN: 41482

American (AMR) AF: 0.717 AC: 10964 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2537 AN: 3472

East Asian (EAS) AF: 0.651 AC: 3362 AN: 5164

South Asian (SAS) AF: 0.587 AC: 2824 AN: 4810

European-Finnish (FIN) AF: 0.811 AC: 8584 AN: 10586

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53588 AN: 67978

Other (OTH) AF: 0.746 AC: 1575 AN: 2112

Alfa AF: 0.767 Hom.: 77686

Bravo AF: 0.746

Asia WGS AF: 0.663 AC: 2305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.3
DANN	Benign	0.68
PhyloP100		0.0040
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7625035;

hg19: chr3-133727866;