6-3271554-C-G
Position:
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
NM_015482.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.68
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]
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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC22A23 | ENST00000406686 | c.*1501G>C | 3_prime_UTR_variant | 10/10 | 5 | NM_015482.2 | ENSP00000385028.3 | |||
SLC22A23 | ENST00000436008 | c.*1501G>C | 3_prime_UTR_variant | 11/11 | 5 | ENSP00000410245.2 | ||||
PSMG4 | ENST00000454610.2 | c.135+12358C>G | intron_variant | 2 | ENSP00000415768.2 | |||||
PSMG4 | ENST00000451246.2 | c.175-10682C>G | intron_variant | 3 | ENSP00000407702.2 |
Frequencies
GnomAD3 genomes AF: 0.654 AC: 99441AN: 152048Hom.: 38747 Cov.: 32
GnomAD3 genomes
AF:
AC:
99441
AN:
152048
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.786 AC: 143AN: 182Hom.: 58 Cov.: 0 AF XY: 0.741 AC XY: 80AN XY: 108
GnomAD4 exome
AF:
AC:
143
AN:
182
Hom.:
Cov.:
0
AF XY:
AC XY:
80
AN XY:
108
Gnomad4 AFR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.654 AC: 99458AN: 152168Hom.: 38754 Cov.: 32 AF XY: 0.658 AC XY: 48972AN XY: 74410
GnomAD4 genome
AF:
AC:
99458
AN:
152168
Hom.:
Cov.:
32
AF XY:
AC XY:
48972
AN XY:
74410
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2101
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at