11-63297311-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001039752.4(SLC22A10):c.515G>A(p.Arg172Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00013 in 1,605,144 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00013 ( 0 hom. )
Consequence
SLC22A10
NM_001039752.4 missense
NM_001039752.4 missense
Scores
7
7
5
Clinical Significance
Conservation
PhyloP100: 6.22
Genes affected
SLC22A10 (HGNC:18057): (solute carrier family 22 member 10) Predicted to enable transmembrane transporter activity. Predicted to be involved in organic anion transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.91
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC22A10 | NM_001039752.4 | c.515G>A | p.Arg172Gln | missense_variant | 3/10 | ENST00000332793.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A10 | ENST00000332793.11 | c.515G>A | p.Arg172Gln | missense_variant | 3/10 | 1 | NM_001039752.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152076Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000128 AC: 31AN: 241452Hom.: 0 AF XY: 0.000122 AC XY: 16AN XY: 130854
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GnomAD4 exome AF: 0.000126 AC: 183AN: 1452950Hom.: 0 Cov.: 29 AF XY: 0.000123 AC XY: 89AN XY: 722388
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GnomAD4 genome AF: 0.000164 AC: 25AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74416
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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 | May 18, 2023 | The c.515G>A (p.R172Q) alteration is located in exon 3 (coding exon 3) of the SLC22A10 gene. This alteration results from a G to A substitution at nucleotide position 515, causing the arginine (R) at amino acid position 172 to be replaced by a glutamine (Q). 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
Uncertain
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Pathogenic
DEOGEN2
Uncertain
D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Pathogenic
D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
H
MutationTaster
Benign
D;D;N;N
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Pathogenic
Sift
Uncertain
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MVP
MPC
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