Genetic Variant SLC22A2:c.*360A>T (chr6-160217072-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003058.4(SLC22A2):c.*360A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 174,332 control chromosomes in the GnomAD database, including 1,401 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 0.12 ( 1262 hom., cov: 33)

Exomes 𝑓: 0.11 ( 139 hom. )

Consequence

SLC22A2
NM_003058.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.09

Publications

15 publications found

Variant links:

Genes affected

SLC22A2 (HGNC:10966): (solute carrier family 22 member 2) Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. It is found primarily in the kidney, where it may mediate the first step in cation reabsorption. [provided by RefSeq, Jul 2008]

SLC22A2 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A2	NM_003058.4 link	c.*360A>T		3_prime_UTR_variant	Exon 11 of 11	ENST00000366953.8	NP_003049.2	O15244-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC22A2	ENST00000366953.8 link	c.*360A>T	3_prime_UTR_variant	Exon 11 of 11	1	NM_003058.4	ENSP00000355920.3	O15244-1
SLC22A2	ENST00000498556.1 link	n.677A>T	non_coding_transcript_exon_variant	Exon 3 of 3	5
SLC22A2	ENST00000486916.5 link	n.640+7633A>T	intron_variant	Intron 5 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18369

AN:

152038

Hom.:

1262

Cov.:

show subpopulations

Gnomad AFR

AF:

0.163

Gnomad AMI

AF:

0.0757

Gnomad AMR

AF:

0.0851

Gnomad ASJ

AF:

0.0510

Gnomad EAS

AF:

0.0448

Gnomad SAS

AF:

0.0836

Gnomad FIN

AF:

0.0937

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.108

GnomAD4 exome

AF:

0.109

AC:

2415

AN:

22176

Hom.:

139

Cov.:

AF XY:

0.108

AC XY:

1211

AN XY:

11264

show subpopulations

African (AFR)

AF:

0.163

AC:

165

AN:

1014

American (AMR)

AF:

0.0661

AC:

AN:

696

Ashkenazi Jewish (ASJ)

AF:

0.0524

AC:

AN:

1012

East Asian (EAS)

AF:

0.0345

AC:

AN:

1564

South Asian (SAS)

AF:

0.0990

AC:

AN:

192

European-Finnish (FIN)

AF:

0.122

AC:

AN:

800

Middle Eastern (MID)

AF:

0.0814

AC:

AN:

European-Non Finnish (NFE)

AF:

0.120

AC:

1817

AN:

15200

Other (OTH)

AF:

0.0968

AC:

156

AN:

1612

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

109

218

326

435

544

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.121

AC:

18380

AN:

152156

Hom.:

1262

Cov.:

AF XY:

0.118

AC XY:

8745

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.163

AC:

6761

AN:

41464

American (AMR)

AF:

0.0848

AC:

1296

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0510

AC:

177

AN:

3472

East Asian (EAS)

AF:

0.0447

AC:

232

AN:

5190

South Asian (SAS)

AF:

0.0843

AC:

407

AN:

4828

European-Finnish (FIN)

AF:

0.0937

AC:

993

AN:

10600

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.121

AC:

8199

AN:

67996

Other (OTH)

AF:

0.107

AC:

226

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

812

1624

2436

3248

4060

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

206

412

618

824

1030

<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:

0.112

Hom.:

599

Bravo

AF:

0.120

Asia WGS

AF:

0.0730

AC:

252

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.7

(source)

DANN

Benign

0.77

PhyloP100

1.1

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