11-63297311-G-A

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

Scores

7
7
5

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.22
Variant links:
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]

Genome browser will be placed here

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
SLC22A10NM_001039752.4 linkuse as main transcriptc.515G>A p.Arg172Gln missense_variant 3/10 ENST00000332793.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC22A10ENST00000332793.11 linkuse as main transcriptc.515G>A p.Arg172Gln missense_variant 3/101 NM_001039752.4 P1Q63ZE4-1

Frequencies

GnomAD3 genomes
AF:
0.000164
AC:
25
AN:
152076
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000725
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000197
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000265
Gnomad OTH
AF:
0.000479
GnomAD3 exomes
AF:
0.000128
AC:
31
AN:
241452
Hom.:
0
AF XY:
0.000122
AC XY:
16
AN XY:
130854
show subpopulations
Gnomad AFR exome
AF:
0.000130
Gnomad AMR exome
AF:
0.000183
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000113
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000467
Gnomad NFE exome
AF:
0.000172
Gnomad OTH exome
AF:
0.000171
GnomAD4 exome
AF:
0.000126
AC:
183
AN:
1452950
Hom.:
0
Cov.:
29
AF XY:
0.000123
AC XY:
89
AN XY:
722388
show subpopulations
Gnomad4 AFR exome
AF:
0.000151
Gnomad4 AMR exome
AF:
0.000210
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000505
Gnomad4 SAS exome
AF:
0.0000119
Gnomad4 FIN exome
AF:
0.0000188
Gnomad4 NFE exome
AF:
0.000137
Gnomad4 OTH exome
AF:
0.000183
GnomAD4 genome
AF:
0.000164
AC:
25
AN:
152194
Hom.:
0
Cov.:
32
AF XY:
0.000134
AC XY:
10
AN XY:
74416
show subpopulations
Gnomad4 AFR
AF:
0.0000723
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000265
Gnomad4 OTH
AF:
0.000474
Alfa
AF:
0.000159
Hom.:
0
Bravo
AF:
0.000196
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000356
AC:
3
ExAC
AF:
0.000107
AC:
13
EpiCase
AF:
0.0000549
EpiControl
AF:
0.000119

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 GeneticsMay 18, 2023The 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.24
BayesDel_addAF
Uncertain
0.074
D
BayesDel_noAF
Pathogenic
0.14
CADD
Uncertain
24
DANN
Pathogenic
1.0
DEOGEN2
Uncertain
0.50
D
Eigen
Uncertain
0.54
Eigen_PC
Uncertain
0.29
FATHMM_MKL
Benign
0.57
D
LIST_S2
Uncertain
0.96
D
M_CAP
Benign
0.037
D
MetaRNN
Pathogenic
0.91
D
MetaSVM
Pathogenic
0.90
D
MutationAssessor
Pathogenic
4.2
H
MutationTaster
Benign
1.0
D;D;N;N
PrimateAI
Benign
0.38
T
PROVEAN
Uncertain
-3.8
D
REVEL
Pathogenic
0.76
Sift
Uncertain
0.0010
D
Sift4G
Pathogenic
0.0
D
Polyphen
1.0
D
Vest4
0.75
MVP
0.54
MPC
0.12
ClinPred
0.90
D
GERP RS
3.3
Varity_R
0.91
gMVP
0.86

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.16
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: rs185055343; hg19: chr11-63064783; COSMIC: COSV60421051; API