Genetic Variant SLC22A3:c.*564G>A (chr6-160451620-G-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_021977.4(SLC22A3):c.*564G>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 0.291 in 157,666 control chromosomes in the GnomAD database, including 8,171 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 0.29 ( 7757 hom., cov: 32)

Exomes 𝑓: 0.37 ( 414 hom. )

Consequence

SLC22A3
NM_021977.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.47

Publications

46 publications found

Variant links:

Genes affected

SLC22A3 (HGNC:10967): (solute carrier family 22 member 3) 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. [provided by RefSeq, Jul 2008]

SLC22A3 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021977.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A3	NM_021977.4	MANE Select	c.*564G>A		3_prime_UTR	Exon 11 of 11	NP_068812.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A3	ENST00000275300.3	TSL:1 MANE Select	c.*564G>A		3_prime_UTR	Exon 11 of 11	ENSP00000275300.2

Frequencies

GnomAD3 genomes

AF:

0.288

AC:

43726

AN:

151978

Hom.:

7743

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0858

Gnomad AMI

AF:

0.418

Gnomad AMR

AF:

0.430

Gnomad ASJ

AF:

0.219

Gnomad EAS

AF:

0.462

Gnomad SAS

AF:

0.276

Gnomad FIN

AF:

0.297

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.367

Gnomad OTH

AF:

0.291

GnomAD4 exome

AF:

0.369

AC:

2056

AN:

5570

Hom.:

414

Cov.:

AF XY:

0.369

AC XY:

1066

AN XY:

2890

show subpopulations

African (AFR)

AF:

0.0526

AC:

AN:

American (AMR)

AF:

0.441

AC:

573

AN:

1300

Ashkenazi Jewish (ASJ)

AF:

0.180

AC:

AN:

East Asian (EAS)

AF:

0.416

AC:

138

AN:

332

South Asian (SAS)

AF:

0.220

AC:

103

AN:

468

European-Finnish (FIN)

AF:

0.231

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.367

AC:

1146

AN:

3124

Other (OTH)

AF:

0.358

AC:

AN:

204

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

122

182

243

304

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

102

136

170

<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:

0.288

AC:

43754

AN:

152096

Hom.:

7757

Cov.:

AF XY:

0.286

AC XY:

21230

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.0858

AC:

3562

AN:

41532

American (AMR)

AF:

0.431

AC:

6593

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.219

AC:

760

AN:

3470

East Asian (EAS)

AF:

0.462

AC:

2385

AN:

5164

South Asian (SAS)

AF:

0.276

AC:

1328

AN:

4818

European-Finnish (FIN)

AF:

0.297

AC:

3143

AN:

10570

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.367

AC:

24935

AN:

67948

Other (OTH)

AF:

0.292

AC:

616

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1493

2986

4479

5972

7465

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

442

884

1326

1768

2210

<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:

0.331

Hom.:

12742

Bravo

AF:

0.290

Asia WGS

AF:

0.380

AC:

1317

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.036

(source)

DANN

Benign

0.54

PhyloP100

-1.5

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