Genetic Variant NM_015482.2:c.*3184G>A (chr6-3269871-C-T) – 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.*3184G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 152,870 control chromosomes in the GnomAD database, including 56,103 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 0.86 ( 55877 hom., cov: 34)

Exomes 𝑓: 0.87 ( 226 hom. )

Consequence

SLC22A23
NM_015482.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0600

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:

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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=-0.77).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A23	NM_015482.2 link	c.*3184G>A		3_prime_UTR_variant	Exon 10 of 10	ENST00000406686.8	NP_056297.1	A1A5C7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A23	ENST00000406686.8 link	c.*3184G>A		3_prime_UTR_variant	Exon 10 of 10	5	NM_015482.2	ENSP00000385028.3		A1A5C7-1

Frequencies

GnomAD3 genomes

AF:

0.855

AC:

130154

AN:

152164

Hom.:

55835

Cov.:

show subpopulations

Gnomad AFR

AF:

0.862

Gnomad AMI

AF:

0.895

Gnomad AMR

AF:

0.832

Gnomad ASJ

AF:

0.864

Gnomad EAS

AF:

0.680

Gnomad SAS

AF:

0.768

Gnomad FIN

AF:

0.911

Gnomad MID

AF:

0.728

Gnomad NFE

AF:

0.868

Gnomad OTH

AF:

0.826

GnomAD4 exome

AF:

0.874

AC:

514

AN:

588

Hom.:

226

Cov.:

AF XY:

0.861

AC XY:

298

AN XY:

346

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.809

AC:

110

AN:

136

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.892

AC:

387

AN:

434

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.875

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.452

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:

0.855

AC:

130253

AN:

152282

Hom.:

55877

Cov.:

AF XY:

0.854

AC XY:

63610

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.862

AC:

35807

AN:

41536

American (AMR)

AF:

0.832

AC:

12731

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.864

AC:

2997

AN:

3470

East Asian (EAS)

AF:

0.681

AC:

3524

AN:

5178

South Asian (SAS)

AF:

0.768

AC:

3713

AN:

4834

European-Finnish (FIN)

AF:

0.911

AC:

9655

AN:

10604

Middle Eastern (MID)

AF:

0.731

AC:

215

AN:

294

European-Non Finnish (NFE)

AF:

0.868

AC:

59048

AN:

68034

Other (OTH)

AF:

0.826

AC:

1747

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1012

2024

3035

4047

5059

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

894

1788

2682

3576

4470

<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:

0.862

Hom.:

10058

Bravo

AF:

0.847

Asia WGS

AF:

0.751

AC:

2608

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.73

(source)

DANN

Benign

0.76

PhyloP100

0.060

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over