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GeneBe

11-75165906-G-A

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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.03
Variant links:
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]

Genome browser will be placed here

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=-0.68).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    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=-4.03 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 = 0.0931 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLCO2B1NM_007256.5 linkuse as main transcriptc.405G>A p.Pro135= synonymous_variant 4/14 ENST00000289575.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLCO2B1ENST00000289575.10 linkuse as main transcriptc.405G>A p.Pro135= synonymous_variant 4/141 NM_007256.5 P2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0274
AC:
4164
AN:
152140
Hom.:
200
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0955
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00929
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000397
Gnomad OTH
AF:
0.0177
GnomAD3 exomes
AF:
0.00743
AC:
1867
AN:
251362
Hom.:
78
AF XY:
0.00554
AC XY:
752
AN XY:
135838
show subpopulations
Gnomad AFR exome
AF:
0.0993
Gnomad AMR exome
AF:
0.00541
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000196
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000246
Gnomad OTH exome
AF:
0.00506
GnomAD4 exome
AF:
0.00269
AC:
3936
AN:
1461780
Hom.:
155
Cov.:
31
AF XY:
0.00234
AC XY:
1701
AN XY:
727200
show subpopulations
Gnomad4 AFR exome
AF:
0.0934
Gnomad4 AMR exome
AF:
0.00588
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000209
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000122
Gnomad4 OTH exome
AF:
0.00599
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0274
AC:
4174
AN:
152258
Hom.:
200
Cov.:
33
AF XY:
0.0264
AC XY:
1967
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.0955
Gnomad4 AMR
AF:
0.00928
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000382
Gnomad4 OTH
AF:
0.0175
Alfa
AF:
0.00516
Hom.:
60
Bravo
AF:
0.0313
Asia WGS
AF:
0.00664
AC:
23
AN:
3478
EpiCase
AF:
0.000273
EpiControl
AF:
0.000237

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 testingInvitaeJun 18, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
Cadd
Benign
0.41
Dann
Benign
0.77

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: rs1109407; hg19: chr11-74876951; API