11-2909224-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002555.6(SLC22A18):c.271G>T(p.Ala91Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000325 in 1,539,132 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 34)
Exomes 𝑓: 0.0000029 ( 0 hom. )
Consequence
SLC22A18
NM_002555.6 missense
NM_002555.6 missense
Scores
7
11
Clinical Significance
Conservation
PhyloP100: 2.56
Genes affected
SLC22A18 (HGNC:10964): (solute carrier family 22 member 18) This gene is one of several tumor-suppressing subtransferable fragments located in the imprinted gene domain of 11p15.5, an important tumor-suppressor gene region. Alterations in this region have been associated with the Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian, and breast cancer. This gene is imprinted, with preferential expression from the maternal allele. Mutations in this gene have been found in Wilms' tumor and lung cancer. This protein may act as a transporter of organic cations, and have a role in the transport of chloroquine and quinidine-related compounds in kidney. Several alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC22A18 | NM_002555.6 | c.271G>T | p.Ala91Ser | missense_variant | 4/11 | ENST00000649076.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A18 | ENST00000649076.2 | c.271G>T | p.Ala91Ser | missense_variant | 4/11 | NM_002555.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 34
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000146 AC: 2AN: 136528Hom.: 0 AF XY: 0.0000133 AC XY: 1AN XY: 75226
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GnomAD4 exome AF: 0.00000288 AC: 4AN: 1386930Hom.: 0 Cov.: 36 AF XY: 0.00000146 AC XY: 1AN XY: 685146
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GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74352
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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 submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.271G>T (p.A91S) alteration is located in exon 4 (coding exon 3) of the SLC22A18 gene. This alteration results from a G to T substitution at nucleotide position 271, causing the alanine (A) at amino acid position 91 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;T;T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Uncertain
D
MetaRNN
Uncertain
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;M;.
MutationTaster
Benign
N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;.;N;D
REVEL
Uncertain
Sift
Uncertain
D;D;.;D;T
Sift4G
Benign
T;T;.;T;T
Polyphen
D;D;D;D;.
Vest4
MutPred
Gain of phosphorylation at A91 (P = 0.0587);Gain of phosphorylation at A91 (P = 0.0587);Gain of phosphorylation at A91 (P = 0.0587);Gain of phosphorylation at A91 (P = 0.0587);Gain of phosphorylation at A91 (P = 0.0587);
MVP
MPC
0.58
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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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