6-3271554-C-G

Variant summary

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

The NM_015482.2(SLC22A23):​c.*1501G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 152,350 control chromosomes in the GnomAD database, including 38,812 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 0.65 ( 38754 hom., cov: 32)
Exomes 𝑓: 0.79 ( 58 hom. )

Consequence

SLC22A23
NM_015482.2 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.68
Variant links:
Genes affected
SLC22A23 (HGNC:21106): (solute carrier family 22 member 23) SLC22A23 belongs to a large family of transmembrane proteins that function as uniporters, symporters, and antiporters to transport organic ions across cell membranes (Jacobsson et al., 2007 [PubMed 17714910]).[supplied by OMIM, Mar 2008]
PSMG4 (HGNC:21108): (proteasome assembly chaperone 4) Predicted to be involved in proteasome assembly. Predicted to be part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC22A23NM_015482.2 linkc.*1501G>C 3_prime_UTR_variant 10/10 ENST00000406686.8 NP_056297.1 A1A5C7-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC22A23ENST00000406686 linkc.*1501G>C 3_prime_UTR_variant 10/105 NM_015482.2 ENSP00000385028.3 A1A5C7-1
SLC22A23ENST00000436008 linkc.*1501G>C 3_prime_UTR_variant 11/115 ENSP00000410245.2 C9J4Z0
PSMG4ENST00000454610.2 linkc.135+12358C>G intron_variant 2 ENSP00000415768.2 H7C465
PSMG4ENST00000451246.2 linkc.175-10682C>G intron_variant 3 ENSP00000407702.2 D6REN3

Frequencies

GnomAD3 genomes
AF:
0.654
AC:
99441
AN:
152048
Hom.:
38747
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.206
Gnomad AMI
AF:
0.844
Gnomad AMR
AF:
0.746
Gnomad ASJ
AF:
0.818
Gnomad EAS
AF:
0.592
Gnomad SAS
AF:
0.638
Gnomad FIN
AF:
0.923
Gnomad MID
AF:
0.611
Gnomad NFE
AF:
0.858
Gnomad OTH
AF:
0.670
GnomAD4 exome
AF:
0.786
AC:
143
AN:
182
Hom.:
58
Cov.:
0
AF XY:
0.741
AC XY:
80
AN XY:
108
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 ASJ exome
AF:
1.00
Gnomad4 EAS exome
AF:
0.793
Gnomad4 FIN exome
AF:
0.900
Gnomad4 NFE exome
AF:
0.667
Gnomad4 OTH exome
AF:
0.875
GnomAD4 genome
AF:
0.654
AC:
99458
AN:
152168
Hom.:
38754
Cov.:
32
AF XY:
0.658
AC XY:
48972
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.206
Gnomad4 AMR
AF:
0.747
Gnomad4 ASJ
AF:
0.818
Gnomad4 EAS
AF:
0.593
Gnomad4 SAS
AF:
0.638
Gnomad4 FIN
AF:
0.923
Gnomad4 NFE
AF:
0.858
Gnomad4 OTH
AF:
0.669
Alfa
AF:
0.661
Hom.:
2636
Bravo
AF:
0.621
Asia WGS
AF:
0.604
AC:
2101
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.026
DANN
Benign
0.49

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: rs3211066; hg19: chr6-3271788; API