Genetic Variant SLC22A23:c.*1501G>C (chr6-3271554-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.68

Publications

3 publications found

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]

SLC22A23 links:

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]

PSMG4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015482.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC22A23	NM_015482.2	MANE Select	c.*1501G>C	3_prime_UTR	Exon 10 of 10	NP_056297.1	A1A5C7-1
SLC22A23	NM_001286455.1		c.*1501G>C	3_prime_UTR	Exon 10 of 10	NP_001273384.1	A1A5C7-2
SLC22A23	NM_021945.6		c.*1501G>C	3_prime_UTR	Exon 11 of 11	NP_068764.3	A1A5C7-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC22A23	ENST00000406686.8	TSL:5 MANE Select	c.*1501G>C	3_prime_UTR	Exon 10 of 10	ENSP00000385028.3	A1A5C7-1
SLC22A23	ENST00000436008.6	TSL:5	c.*1501G>C	3_prime_UTR	Exon 11 of 11	ENSP00000410245.2	C9J4Z0
PSMG4	ENST00000884818.1		c.*40+3802C>G	intron	N/A	ENSP00000554877.1

Frequencies

GnomAD3 genomes

AF:

0.654

AC:

99441

AN:

152048

Hom.:

38747

Cov.:

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.:

Cov.:

AF XY:

0.741

AC XY:

AN XY:

108

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.793

AC:

111

AN:

140

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.900

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.667

AC:

AN:

Other (OTH)

AF:

0.875

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.654

AC:

99458

AN:

152168

Hom.:

38754

Cov.:

AF XY:

0.658

AC XY:

48972

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.206

AC:

8557

AN:

41506

American (AMR)

AF:

0.747

AC:

11417

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.818

AC:

2838

AN:

3468

East Asian (EAS)

AF:

0.593

AC:

3057

AN:

5158

South Asian (SAS)

AF:

0.638

AC:

3076

AN:

4820

European-Finnish (FIN)

AF:

0.923

AC:

9792

AN:

10610

Middle Eastern (MID)

AF:

0.616

AC:

181

AN:

294

European-Non Finnish (NFE)

AF:

0.858

AC:

58358

AN:

67996

Other (OTH)

AF:

0.669

AC:

1412

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1147

2293

3440

4586

5733

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

742

1484

2226

2968

3710

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.026

(source)

DANN

Benign

0.49

PhyloP100

-3.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over