Menu
GeneBe

11-75165941-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_007256.5(SLCO2B1):c.440C>A(p.Thr147Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

SLCO2B1
NM_007256.5 missense

Scores

17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.529
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 Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08936262).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLCO2B1NM_007256.5 linkuse as main transcriptc.440C>A p.Thr147Asn missense_variant 4/14 ENST00000289575.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLCO2B1ENST00000289575.10 linkuse as main transcriptc.440C>A p.Thr147Asn missense_variant 4/141 NM_007256.5 P2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
33

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsAug 10, 2021The c.440C>A (p.T147N) alteration is located in exon 4 (coding exon 4) of the SLCO2B1 gene. This alteration results from a C to A substitution at nucleotide position 440, causing the threonine (T) at amino acid position 147 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.079
BayesDel_addAF
Benign
-0.28
T
BayesDel_noAF
Benign
-0.64
Cadd
Benign
3.7
Dann
Benign
0.79
Eigen
Benign
-0.99
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.040
N
LIST_S2
Benign
0.69
T;T;.;T;T;.;T
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.089
T;T;T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationTaster
Benign
1.0
N;N;N;N;N;N;N
PrimateAI
Benign
0.29
T
PROVEAN
Benign
-1.4
N;N;N;N;N;N;N
REVEL
Benign
0.029
Sift
Benign
0.077
T;T;T;T;T;T;T
Sift4G
Benign
0.21
T;T;T;T;T;T;T
Vest4
0.11
MutPred
0.38
Loss of phosphorylation at T147 (P = 0.0506);.;.;.;.;.;.;
MVP
0.40
MPC
0.27
ClinPred
0.13
T
GERP RS
0.45
gMVP
0.32

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-74876986; COSMIC: COSV56938685; COSMIC: COSV56938685; API