rs1109407
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_007256.5(SLCO2B1):c.405G>A(p.Pro135=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00502 in 1,614,038 control chromosomes in the GnomAD database, including 355 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.027 ( 200 hom., cov: 33)
Exomes 𝑓: 0.0027 ( 155 hom. )
Consequence
SLCO2B1
NM_007256.5 synonymous
NM_007256.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.03
Genes affected
SLCO2B1 (HGNC:10962): (solute carrier organic anion transporter family member 2B1) This locus encodes a member of the organic anion-transporting polypeptide family of membrane proteins. The protein encoded by this locus may function in regulation of placental uptake of sulfated steroids. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
?
Variant 11-75165906-G-A is Benign according to our data. Variant chr11-75165906-G-A is described in ClinVar as [Benign]. Clinvar id is 783634.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-4.03 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0931 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO2B1 | NM_007256.5 | c.405G>A | p.Pro135= | synonymous_variant | 4/14 | ENST00000289575.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO2B1 | ENST00000289575.10 | c.405G>A | p.Pro135= | synonymous_variant | 4/14 | 1 | NM_007256.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0274 AC: 4164AN: 152140Hom.: 200 Cov.: 33
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GnomAD3 exomes AF: 0.00743 AC: 1867AN: 251362Hom.: 78 AF XY: 0.00554 AC XY: 752AN XY: 135838
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GnomAD4 exome AF: 0.00269 AC: 3936AN: 1461780Hom.: 155 Cov.: 31 AF XY: 0.00234 AC XY: 1701AN XY: 727200
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GnomAD4 genome ? AF: 0.0274 AC: 4174AN: 152258Hom.: 200 Cov.: 33 AF XY: 0.0264 AC XY: 1967AN XY: 74446
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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 submitter | clinical testing | Invitae | Jun 18, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at