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GeneBe

6-160224731-G-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_003058.4(SLC22A2):c.1575C>A(p.Thr525=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00694 in 1,605,200 control chromosomes in the GnomAD database, including 54 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0047 ( 5 hom., cov: 32)
Exomes 𝑓: 0.0072 ( 49 hom. )

Consequence

SLC22A2
NM_003058.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.382
Variant links:
Genes affected
SLC22A2 (HGNC:10966): (solute carrier family 22 member 2) Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. It is found primarily in the kidney, where it may mediate the first step in cation reabsorption. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 6-160224731-G-T is Benign according to our data. Variant chr6-160224731-G-T is described in ClinVar as [Benign]. Clinvar id is 774649.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.382 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 5 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC22A2NM_003058.4 linkuse as main transcriptc.1575C>A p.Thr525= synonymous_variant 10/11 ENST00000366953.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC22A2ENST00000366953.8 linkuse as main transcriptc.1575C>A p.Thr525= synonymous_variant 10/111 NM_003058.4 P1O15244-1
SLC22A2ENST00000486916.5 linkuse as main transcriptn.614C>A non_coding_transcript_exon_variant 5/63
SLC22A2ENST00000491092.1 linkuse as main transcriptn.1472C>A non_coding_transcript_exon_variant 9/105

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00475
AC:
723
AN:
152080
Hom.:
5
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00147
Gnomad AMI
AF:
0.0329
Gnomad AMR
AF:
0.00164
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000622
Gnomad FIN
AF:
0.00217
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00845
Gnomad OTH
AF:
0.00287
GnomAD3 exomes
AF:
0.00419
AC:
1036
AN:
247340
Hom.:
4
AF XY:
0.00415
AC XY:
555
AN XY:
133710
show subpopulations
Gnomad AFR exome
AF:
0.00112
Gnomad AMR exome
AF:
0.00160
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00121
Gnomad FIN exome
AF:
0.00227
Gnomad NFE exome
AF:
0.00761
Gnomad OTH exome
AF:
0.00367
GnomAD4 exome
AF:
0.00717
AC:
10421
AN:
1453002
Hom.:
49
Cov.:
29
AF XY:
0.00705
AC XY:
5092
AN XY:
722666
show subpopulations
Gnomad4 AFR exome
AF:
0.000901
Gnomad4 AMR exome
AF:
0.00178
Gnomad4 ASJ exome
AF:
0.0000771
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00124
Gnomad4 FIN exome
AF:
0.00243
Gnomad4 NFE exome
AF:
0.00883
Gnomad4 OTH exome
AF:
0.00504
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00474
AC:
721
AN:
152198
Hom.:
5
Cov.:
32
AF XY:
0.00415
AC XY:
309
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.00147
Gnomad4 AMR
AF:
0.00164
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00217
Gnomad4 NFE
AF:
0.00845
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00623
Hom.:
3
Bravo
AF:
0.00471
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 31, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
Cadd
Benign
1.2
Dann
Benign
0.65

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: rs139737555; hg19: chr6-160645763; API