dbSNP rs4149178: SLC22A7:c.*172A>G (chr6-43304450-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000372574.7(SLC22A7):c.*172A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 588,666 control chromosomes in the GnomAD database, including 10,622 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 0.21 ( 4063 hom., cov: 33)

Exomes 𝑓: 0.16 ( 6559 hom. )

Consequence

SLC22A7
ENST00000372574.7 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0660

Publications

40 publications found

Variant links:

Genes affected

SLC22A7 (HGNC:10971): (solute carrier family 22 member 7) The protein encoded by this gene is involved in the sodium-independent transport and excretion of organic anions, some of which are potentially toxic. The encoded protein is an integral membrane protein and appears to be localized to the basolateral membrane of the kidney. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

SLC22A7 links:

CRIP3 (HGNC:17751): (cysteine rich protein 3) Predicted to enable metal ion binding activity. Predicted to act upstream of or within T cell proliferation. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

CRIP3 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A7	NM_153320.2 link	c.1592+206A>G		intron_variant	Intron 10 of 10	ENST00000372585.10	NP_696961.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A7	ENST00000372585.10 link	c.1592+206A>G		intron_variant	Intron 10 of 10	5	NM_153320.2	ENSP00000361666.5

Frequencies

GnomAD3 genomes

AF:

0.212

AC:

32192

AN:

152014

Hom.:

4052

Cov.:

show subpopulations

Gnomad AFR

AF:

0.347

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.225

Gnomad EAS

AF:

0.0477

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.264

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.229

GnomAD4 exome

AF:

0.163

AC:

71268

AN:

436534

Hom.:

6559

Cov.:

AF XY:

0.163

AC XY:

37235

AN XY:

227908

show subpopulations

African (AFR)

AF:

0.345

AC:

3961

AN:

11494

American (AMR)

AF:

0.228

AC:

3232

AN:

14164

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

2688

AN:

12938

East Asian (EAS)

AF:

0.0556

AC:

1556

AN:

27992

South Asian (SAS)

AF:

0.168

AC:

6402

AN:

38182

European-Finnish (FIN)

AF:

0.149

AC:

4751

AN:

31792

Middle Eastern (MID)

AF:

0.242

AC:

854

AN:

3526

European-Non Finnish (NFE)

AF:

0.159

AC:

43255

AN:

271438

Other (OTH)

AF:

0.183

AC:

4569

AN:

25008

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

3090

6181

9271

12362

15452

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

464

928

1392

1856

2320

<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:

0.212

AC:

32247

AN:

152132

Hom.:

4063

Cov.:

AF XY:

0.208

AC XY:

15461

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.347

AC:

14374

AN:

41430

American (AMR)

AF:

0.207

AC:

3158

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.225

AC:

781

AN:

3472

East Asian (EAS)

AF:

0.0480

AC:

249

AN:

5186

South Asian (SAS)

AF:

0.156

AC:

754

AN:

4830

European-Finnish (FIN)

AF:

0.136

AC:

1442

AN:

10614

Middle Eastern (MID)

AF:

0.250

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.159

AC:

10824

AN:

67990

Other (OTH)

AF:

0.228

AC:

482

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1293

2587

3880

5174

6467

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

328

656

984

1312

1640

<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:

0.178

Hom.:

5111

Bravo

AF:

0.224

Asia WGS

AF:

0.122

AC:

423

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.5

(source)

DANN

Benign

0.38

PhyloP100

0.066

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