3-133934794-G-C
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_005630.3(SLCO2A1):āc.1851C>Gā(p.Gly617Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,076 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Consequence
SLCO2A1
NM_005630.3 synonymous
NM_005630.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.254
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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 3-133934794-G-C is Benign according to our data. Variant chr3-133934794-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2133923.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.254 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLCO2A1 | NM_005630.3 | c.1851C>G | p.Gly617Gly | synonymous_variant | 14/14 | ENST00000310926.11 | NP_005621.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLCO2A1 | ENST00000310926.11 | c.1851C>G | p.Gly617Gly | synonymous_variant | 14/14 | 1 | NM_005630.3 | ENSP00000311291.4 | ||
SLCO2A1 | ENST00000493729.5 | c.1623C>G | p.Gly541Gly | synonymous_variant | 13/13 | 5 | ENSP00000418893.1 | |||
SLCO2A1 | ENST00000481359.3 | n.*413C>G | non_coding_transcript_exon_variant | 13/13 | 5 | ENSP00000420028.3 | ||||
SLCO2A1 | ENST00000481359.3 | n.*413C>G | 3_prime_UTR_variant | 13/13 | 5 | ENSP00000420028.3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152076Hom.: 0 Cov.: 32
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GnomAD4 exome Cov.: 30
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GnomAD4 genome AF: 0.00000658 AC: 1AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74268
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 18, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at