rs7616492

Positions:

• chr3-133936002-G-A
• chr3-133936002-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_005630.3(SLCO2A1):​c.1691-105C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 1,198,494 control chromosomes in the GnomAD database, including 79,589 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.28 (7152 hom., cov: 32)
  • Exomes 𝑓: 0.37 (72437 hom.)
• Consequence: SLCO2A1 NM_005630.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.84

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 3-133936002-G-A is Benign according to our data. Variant chr3-133936002-G-A is described in ClinVar as [Benign]. Clinvar id is 1177670.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO2A1	NM_005630.3	c.1691-105C>T		intron_variant		ENST00000310926.11	NP_005621.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO2A1	ENST00000310926.11	c.1691-105C>T		intron_variant		1	NM_005630.3	ENSP00000311291	P1
SLCO2A1	ENST00000493729.5	c.1463-105C>T		intron_variant		5		ENSP00000418893
SLCO2A1	ENST00000481359.3	c.*253-105C>T		intron_variant, NMD_transcript_variant		5		ENSP00000420028

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42264 AN: 152016 Hom.: 7156 Cov.: 32

Gnomad AFR AF: 0.0804

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.307

GnomAD4 exome AF: 0.365 AC: 382108 AN: 1046360 Hom.: 72437 AF XY: 0.364 AC XY: 184022 AN XY: 505648

Gnomad4 AFR exome AF: 0.0713

Gnomad4 AMR exome AF: 0.301

Gnomad4 ASJ exome AF: 0.361

Gnomad4 EAS exome AF: 0.276

Gnomad4 SAS exome AF: 0.232

Gnomad4 FIN exome AF: 0.339

Gnomad4 NFE exome AF: 0.387

Gnomad4 OTH exome AF: 0.337

GnomAD4 genome AF: 0.278 AC: 42257 AN: 152134 Hom.: 7152 Cov.: 32 AF XY: 0.274 AC XY: 20379 AN XY: 74370

Gnomad4 AFR AF: 0.0802

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.307

Alfa AF: 0.371 Hom.: 17410

Bravo AF: 0.272

Asia WGS AF: 0.221 AC: 771 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.019
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7616492; hg19: chr3-133654846; COSMIC: COSV60491140;