rs316024

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000366952.1(SLC22A2):​c.-1296-518G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,032 control chromosomes in the GnomAD database, including 8,575 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.32 ( 8575 hom., cov: 32)

Consequence

SLC22A2
ENST00000366952.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.747
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.160261205C>T intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC22A2ENST00000366952.1 linkuse as main transcriptc.-1296-518G>A intron_variant 5 ENSP00000355919.1 Q5T7Q5

Frequencies

GnomAD3 genomes
AF:
0.323
AC:
49112
AN:
151914
Hom.:
8560
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.227
Gnomad AMI
AF:
0.232
Gnomad AMR
AF:
0.497
Gnomad ASJ
AF:
0.283
Gnomad EAS
AF:
0.453
Gnomad SAS
AF:
0.380
Gnomad FIN
AF:
0.377
Gnomad MID
AF:
0.225
Gnomad NFE
AF:
0.324
Gnomad OTH
AF:
0.315
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.323
AC:
49153
AN:
152032
Hom.:
8575
Cov.:
32
AF XY:
0.331
AC XY:
24640
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.227
Gnomad4 AMR
AF:
0.498
Gnomad4 ASJ
AF:
0.283
Gnomad4 EAS
AF:
0.453
Gnomad4 SAS
AF:
0.381
Gnomad4 FIN
AF:
0.377
Gnomad4 NFE
AF:
0.324
Gnomad4 OTH
AF:
0.318
Alfa
AF:
0.331
Hom.:
10013
Bravo
AF:
0.328
Asia WGS
AF:
0.409
AC:
1423
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
3.8
DANN
Benign
0.60

Splicing

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: rs316024; hg19: chr6-160682237; API