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GeneBe

11-75163968-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7

The NM_007256.5(SLCO2B1):c.153C>T(p.Phe51=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000219 in 1,598,572 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00081 ( 1 hom., cov: 31)
Exomes 𝑓: 0.00016 ( 0 hom. )

Consequence

SLCO2B1
NM_007256.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.661
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
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=-0.4).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-75163968-C-T is Benign according to our data. Variant chr11-75163968-C-T is described in ClinVar as [Benign]. Clinvar id is 745676.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=0.661 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLCO2B1NM_007256.5 linkuse as main transcriptc.153C>T p.Phe51= synonymous_variant 3/14 ENST00000289575.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLCO2B1ENST00000289575.10 linkuse as main transcriptc.153C>T p.Phe51= synonymous_variant 3/141 NM_007256.5 P2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000815
AC:
124
AN:
152194
Hom.:
1
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00278
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.000957
GnomAD3 exomes
AF:
0.000309
AC:
69
AN:
223534
Hom.:
0
AF XY:
0.000290
AC XY:
35
AN XY:
120622
show subpopulations
Gnomad AFR exome
AF:
0.00303
Gnomad AMR exome
AF:
0.000124
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000838
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.000178
GnomAD4 exome
AF:
0.000156
AC:
226
AN:
1446378
Hom.:
0
Cov.:
31
AF XY:
0.000173
AC XY:
124
AN XY:
718122
show subpopulations
Gnomad4 AFR exome
AF:
0.00334
Gnomad4 AMR exome
AF:
0.000163
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000994
Gnomad4 FIN exome
AF:
0.0000574
Gnomad4 NFE exome
AF:
0.00000453
Gnomad4 OTH exome
AF:
0.000301
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000815
AC:
124
AN:
152194
Hom.:
1
Cov.:
31
AF XY:
0.000713
AC XY:
53
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.00278
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000621
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.000957
Alfa
AF:
0.000356
Hom.:
0
Bravo
AF:
0.000907
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

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 01, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
Cadd
Benign
4.9
Dann
Benign
0.77

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.20
Details are displayed if max score is > 0.2
DS_AL_spliceai
0.20
Position offset: -5

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: rs138677494; hg19: chr11-74875013; COSMIC: COSV104612867; COSMIC: COSV104612867; API