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11-62981288-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_153276.3(SLC22A6):​c.893G>A​(p.Arg298Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000876 in 1,609,026 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00018 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000078 ( 0 hom. )

Consequence

SLC22A6
NM_153276.3 missense

Scores

18

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.51
Variant links:
Genes affected
SLC22A6 (HGNC:10970): (solute carrier family 22 member 6) The protein encoded by this gene is involved in the sodium-dependent transport and excretion of organic anions, some of which are potentially toxic. The encoded protein is an integral membrane protein and may be localized to the basolateral membrane. Four transcript variants encoding four different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.021107078).
BP6
Variant 11-62981288-C-T is Benign according to our data. Variant chr11-62981288-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2389643.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC22A6NM_153276.3 linkuse as main transcriptc.893G>A p.Arg298Gln missense_variant 5/10 ENST00000360421.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC22A6ENST00000360421.9 linkuse as main transcriptc.893G>A p.Arg298Gln missense_variant 5/101 NM_153276.3 P1Q4U2R8-2

Frequencies

GnomAD3 genomes
AF:
0.000171
AC:
26
AN:
152090
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000459
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
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:
0.0000882
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.0000873
AC:
21
AN:
240468
Hom.:
0
AF XY:
0.0000539
AC XY:
7
AN XY:
129802
show subpopulations
Gnomad AFR exome
AF:
0.000326
Gnomad AMR exome
AF:
0.0000598
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000169
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000101
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000783
AC:
114
AN:
1456818
Hom.:
0
Cov.:
33
AF XY:
0.0000760
AC XY:
55
AN XY:
724088
show subpopulations
Gnomad4 AFR exome
AF:
0.000329
Gnomad4 AMR exome
AF:
0.0000909
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000506
Gnomad4 SAS exome
AF:
0.0000706
Gnomad4 FIN exome
AF:
0.0000188
Gnomad4 NFE exome
AF:
0.0000775
Gnomad4 OTH exome
AF:
0.0000664
GnomAD4 genome
AF:
0.000177
AC:
27
AN:
152208
Hom.:
0
Cov.:
32
AF XY:
0.0000940
AC XY:
7
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.000482
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000882
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.000114
Hom.:
0
Bravo
AF:
0.000219
ExAC
AF:
0.000115
AC:
14

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Likely benign, criteria provided, single submitterclinical testingAmbry GeneticsDec 14, 2021This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.071
BayesDel_addAF
Benign
-0.49
T
BayesDel_noAF
Benign
-0.59
CADD
Benign
0.22
DANN
Benign
0.97
Eigen
Benign
-1.0
Eigen_PC
Benign
-0.95
FATHMM_MKL
Benign
0.012
N
LIST_S2
Benign
0.37
T;T;T;T
M_CAP
Benign
0.021
T
MetaRNN
Benign
0.021
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-0.43
N;N;N;N
MutationTaster
Benign
1.0
N;N;N;N
PrimateAI
Benign
0.21
T
PROVEAN
Benign
-0.040
N;N;N;N
REVEL
Benign
0.038
Sift
Benign
0.36
T;T;T;T
Sift4G
Benign
0.29
T;T;T;T
Polyphen
0.0
B;B;B;B
Vest4
0.14
MutPred
0.40
Loss of MoRF binding (P = 0.052);Loss of MoRF binding (P = 0.052);Loss of MoRF binding (P = 0.052);Loss of MoRF binding (P = 0.052);
MVP
0.37
MPC
0.20
ClinPred
0.044
T
GERP RS
-2.0
Varity_R
0.036
gMVP
0.065

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs776644088; hg19: chr11-62748760; API