dbSNP rs2470984: SLC13A1:c.813-146G>T (chr7-123134675-C-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_022444.4(SLC13A1):c.813-146G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 584,892 control chromosomes in the GnomAD database, including 28,241 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 0.36 ( 10476 hom., cov: 31)

Exomes 𝑓: 0.28 ( 17765 hom. )

Consequence

SLC13A1
NM_022444.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.345

Publications

4 publications found

Variant links:

Genes affected

SLC13A1 (HGNC:10916): (solute carrier family 13 member 1) The protein encoded by this gene is an apical membrane Na(+)-sulfate cotransporter involved in sulfate homeostasis in the kidney. Defects in this gene lead to many pathophysiologic problems. [provided by RefSeq, May 2016]

SLC13A1 Gene-Disease associations (from GenCC):

sulfation-related bone disorder
Inheritance: AR Classification: MODERATE Submitted by: PanelApp Australia

SLC13A1 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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022444.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC13A1	NM_022444.4	MANE Select	c.813-146G>T		intron	N/A	NP_071889.2
	SLC13A1	NM_001324400.1		c.441-146G>T		intron	N/A	NP_001311329.1	Q2NKK0

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC13A1	ENST00000194130.7	TSL:1 MANE Select	c.813-146G>T	intron	N/A	ENSP00000194130.2	Q9BZW2
SLC13A1	ENST00000439260.5	TSL:1	n.*1191-146G>T	intron	N/A	ENSP00000401417.1	F8WEM4
SLC13A1	ENST00000954470.1		c.813-146G>T	intron	N/A	ENSP00000624529.1

Frequencies

GnomAD3 genomes

AF:

0.355

AC:

53897

AN:

151800

Hom.:

10441

Cov.:

show subpopulations

Gnomad AFR

AF:

0.516

Gnomad AMI

AF:

0.172

Gnomad AMR

AF:

0.303

Gnomad ASJ

AF:

0.242

Gnomad EAS

AF:

0.292

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.334

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.291

Gnomad OTH

AF:

0.338

GnomAD4 exome

AF:

0.276

AC:

119691

AN:

432974

Hom.:

17765

AF XY:

0.276

AC XY:

61412

AN XY:

222900

show subpopulations

African (AFR)

AF:

0.503

AC:

5540

AN:

11004

American (AMR)

AF:

0.240

AC:

3115

AN:

12960

Ashkenazi Jewish (ASJ)

AF:

0.230

AC:

2585

AN:

11248

East Asian (EAS)

AF:

0.255

AC:

6881

AN:

26952

South Asian (SAS)

AF:

0.244

AC:

6195

AN:

25344

European-Finnish (FIN)

AF:

0.310

AC:

9030

AN:

29120

Middle Eastern (MID)

AF:

0.338

AC:

957

AN:

2834

European-Non Finnish (NFE)

AF:

0.270

AC:

78333

AN:

290048

Other (OTH)

AF:

0.301

AC:

7055

AN:

23464

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

3988

7975

11963

15950

19938

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1370

2740

4110

5480

6850

<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:

0.355

AC:

53991

AN:

151918

Hom.:

10476

Cov.:

AF XY:

0.356

AC XY:

26405

AN XY:

74232

show subpopulations

African (AFR)

AF:

0.516

AC:

21373

AN:

41412

American (AMR)

AF:

0.302

AC:

4616

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.242

AC:

839

AN:

3470

East Asian (EAS)

AF:

0.293

AC:

1508

AN:

5150

South Asian (SAS)

AF:

0.292

AC:

1403

AN:

4812

European-Finnish (FIN)

AF:

0.334

AC:

3520

AN:

10538

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.291

AC:

19751

AN:

67966

Other (OTH)

AF:

0.347

AC:

731

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1639

3277

4916

6554

8193

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

506

1012

1518

2024

2530

<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:

0.298

Hom.:

12165

Bravo

AF:

0.361

Asia WGS

AF:

0.360

AC:

1255

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.32

(source)

DANN

Benign

0.35

PhyloP100

-0.34

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