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GeneBe

6-3273379-C-T

Variant summary

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

The NM_015482.2(SLC22A23):c.1737G>A(p.Ala579=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00486 in 1,612,764 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0035 ( 3 hom., cov: 33)
Exomes 𝑓: 0.0050 ( 22 hom. )

Consequence

SLC22A23
NM_015482.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.86
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 -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=-0.58).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 6-3273379-C-T is Benign according to our data. Variant chr6-3273379-C-T is described in ClinVar as [Benign]. Clinvar id is 790986.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=-1.86 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 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC22A23NM_015482.2 linkuse as main transcriptc.1737G>A p.Ala579= synonymous_variant 10/10 ENST00000406686.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC22A23ENST00000406686.8 linkuse as main transcriptc.1737G>A p.Ala579= synonymous_variant 10/105 NM_015482.2 P2A1A5C7-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00350
AC:
533
AN:
152226
Hom.:
3
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000844
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00412
Gnomad ASJ
AF:
0.00403
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.000827
Gnomad FIN
AF:
0.00536
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00522
Gnomad OTH
AF:
0.00191
GnomAD3 exomes
AF:
0.00332
AC:
816
AN:
245874
Hom.:
2
AF XY:
0.00330
AC XY:
441
AN XY:
133784
show subpopulations
Gnomad AFR exome
AF:
0.000625
Gnomad AMR exome
AF:
0.00194
Gnomad ASJ exome
AF:
0.00170
Gnomad EAS exome
AF:
0.0000545
Gnomad SAS exome
AF:
0.00134
Gnomad FIN exome
AF:
0.00324
Gnomad NFE exome
AF:
0.00541
Gnomad OTH exome
AF:
0.00329
GnomAD4 exome
AF:
0.00501
AC:
7310
AN:
1460420
Hom.:
22
Cov.:
32
AF XY:
0.00496
AC XY:
3603
AN XY:
726532
show subpopulations
Gnomad4 AFR exome
AF:
0.000717
Gnomad4 AMR exome
AF:
0.00192
Gnomad4 ASJ exome
AF:
0.00287
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00154
Gnomad4 FIN exome
AF:
0.00318
Gnomad4 NFE exome
AF:
0.00590
Gnomad4 OTH exome
AF:
0.00446
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00350
AC:
533
AN:
152344
Hom.:
3
Cov.:
33
AF XY:
0.00334
AC XY:
249
AN XY:
74500
show subpopulations
Gnomad4 AFR
AF:
0.000842
Gnomad4 AMR
AF:
0.00412
Gnomad4 ASJ
AF:
0.00403
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000828
Gnomad4 FIN
AF:
0.00536
Gnomad4 NFE
AF:
0.00522
Gnomad4 OTH
AF:
0.00189
Alfa
AF:
0.00274
Hom.:
0
Bravo
AF:
0.00364
Asia WGS
AF:
0.00231
AC:
8
AN:
3478
EpiCase
AF:
0.00463
EpiControl
AF:
0.00415

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 testingInvitaeAug 07, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.58
Cadd
Benign
7.2
Dann
Benign
0.85
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs141353043; hg19: chr6-3273613; API