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3-133934722-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_005630.3(SLCO2A1):c.1923C>T(p.Gly641=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00496 in 1,613,170 control chromosomes in the GnomAD database, including 349 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.025 ( 162 hom., cov: 32)
Exomes 𝑓: 0.0029 ( 187 hom. )

Consequence

SLCO2A1
NM_005630.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.262
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-133934722-G-A is Benign according to our data. Variant chr3-133934722-G-A is described in ClinVar as [Benign]. Clinvar id is 780895.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.262 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.085 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLCO2A1NM_005630.3 linkuse as main transcriptc.1923C>T p.Gly641= synonymous_variant 14/14 ENST00000310926.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLCO2A1ENST00000310926.11 linkuse as main transcriptc.1923C>T p.Gly641= synonymous_variant 14/141 NM_005630.3 P1
SLCO2A1ENST00000493729.5 linkuse as main transcriptc.1695C>T p.Gly565= synonymous_variant 13/135
SLCO2A1ENST00000481359.3 linkuse as main transcriptc.*485C>T 3_prime_UTR_variant, NMD_transcript_variant 13/135

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0251
AC:
3819
AN:
152202
Hom.:
162
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0875
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00890
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.000353
Gnomad OTH
AF:
0.0139
GnomAD3 exomes
AF:
0.00737
AC:
1843
AN:
250226
Hom.:
76
AF XY:
0.00531
AC XY:
719
AN XY:
135352
show subpopulations
Gnomad AFR exome
AF:
0.0991
Gnomad AMR exome
AF:
0.00463
Gnomad ASJ exome
AF:
0.000199
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000398
Gnomad OTH exome
AF:
0.00392
GnomAD4 exome
AF:
0.00285
AC:
4169
AN:
1460850
Hom.:
187
Cov.:
30
AF XY:
0.00239
AC XY:
1737
AN XY:
726780
show subpopulations
Gnomad4 AFR exome
AF:
0.0971
Gnomad4 AMR exome
AF:
0.00494
Gnomad4 ASJ exome
AF:
0.000115
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000209
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000274
Gnomad4 OTH exome
AF:
0.00581
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0251
AC:
3826
AN:
152320
Hom.:
162
Cov.:
32
AF XY:
0.0248
AC XY:
1847
AN XY:
74490
show subpopulations
Gnomad4 AFR
AF:
0.0874
Gnomad4 AMR
AF:
0.00889
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000353
Gnomad4 OTH
AF:
0.0137
Alfa
AF:
0.00540
Hom.:
34
Bravo
AF:
0.0285
Asia WGS
AF:
0.00462
AC:
17
AN:
3476
EpiCase
AF:
0.000436
EpiControl
AF:
0.000296

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 22, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
Cadd
Benign
5.0
Dann
Benign
0.54

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs72978391; hg19: chr3-133653566; API