dbSNP rs4551716: SLC5A12:c.1707+107G>A (chr11-26673295-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_178498.4(SLC5A12):c.1707+107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 1,233,078 control chromosomes in the GnomAD database, including 143,048 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 0.46 ( 16300 hom., cov: 33)

Exomes 𝑓: 0.48 ( 126748 hom. )

Consequence

SLC5A12
NM_178498.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.353

Publications

6 publications found

Variant links:

Genes affected

SLC5A12 (HGNC:28750): (solute carrier family 5 member 12) Normal blood lactate is maintained at about 1.5 mM, and little filtered lactate is excreted in urine. Reabsorption of lactate is mediated by the low-affinity Na(+)-coupled lactate transporter SLC5A12 in the initial part of the proximal tubule and by the high-affinity Na(+)-coupled lactate transporter SLC5A8 (MIM 608044) in the distal proximal tubule (Gopal et al., 2007 [PubMed 17692818]).[supplied by OMIM, Dec 2008]

SLC5A12 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=-1.0).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SLC5A12	NM_178498.4 link	c.1707+107G>A	intron_variant	Intron 14 of 14	ENST00000396005.8	NP_848593.2	Q1EHB4-1
SLC5A12	XM_006718155.4 link	c.1374+107G>A	intron_variant	Intron 14 of 14		XP_006718218.1
SLC5A12	XM_011519920.3 link	c.1143+107G>A	intron_variant	Intron 15 of 15		XP_011518222.1
SLC5A12	XM_017017244.2 link	c.1143+107G>A	intron_variant	Intron 15 of 15		XP_016872733.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC5A12	ENST00000396005.8 link	c.1707+107G>A		intron_variant	Intron 14 of 14	1	NM_178498.4	ENSP00000379326.3		Q1EHB4-1
SLC5A12	ENST00000527405.5 link	n.*313+107G>A		intron_variant	Intron 14 of 14	2		ENSP00000436011.1		G3V1E3

Frequencies

GnomAD3 genomes

AF:

0.459

AC:

69730

AN:

151924

Hom.:

16286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.439

Gnomad AMI

AF:

0.482

Gnomad AMR

AF:

0.364

Gnomad ASJ

AF:

0.523

Gnomad EAS

AF:

0.354

Gnomad SAS

AF:

0.502

Gnomad FIN

AF:

0.397

Gnomad MID

AF:

0.547

Gnomad NFE

AF:

0.503

Gnomad OTH

AF:

0.454

GnomAD4 exome

AF:

0.482

AC:

520683

AN:

1081038

Hom.:

126748

AF XY:

0.483

AC XY:

255398

AN XY:

528570

show subpopulations

African (AFR)

AF:

0.435

AC:

10056

AN:

23120

American (AMR)

AF:

0.289

AC:

5485

AN:

19002

Ashkenazi Jewish (ASJ)

AF:

0.515

AC:

8146

AN:

15820

East Asian (EAS)

AF:

0.373

AC:

11691

AN:

31336

South Asian (SAS)

AF:

0.503

AC:

19949

AN:

39692

European-Finnish (FIN)

AF:

0.412

AC:

16233

AN:

39354

Middle Eastern (MID)

AF:

0.477

AC:

2183

AN:

4576

European-Non Finnish (NFE)

AF:

0.493

AC:

425791

AN:

863312

Other (OTH)

AF:

0.472

AC:

21149

AN:

44826

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

12445

24890

37336

49781

62226

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13088

26176

39264

52352

65440

<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:

0.459

AC:

69778

AN:

152040

Hom.:

16300

Cov.:

AF XY:

0.454

AC XY:

33750

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.438

AC:

18185

AN:

41476

American (AMR)

AF:

0.364

AC:

5554

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.523

AC:

1815

AN:

3468

East Asian (EAS)

AF:

0.354

AC:

1829

AN:

5168

South Asian (SAS)

AF:

0.502

AC:

2426

AN:

4828

European-Finnish (FIN)

AF:

0.397

AC:

4190

AN:

10556

Middle Eastern (MID)

AF:

0.551

AC:

162

AN:

294

European-Non Finnish (NFE)

AF:

0.503

AC:

34219

AN:

67966

Other (OTH)

AF:

0.454

AC:

959

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1990

3980

5969

7959

9949

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

642

1284

1926

2568

3210

<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:

0.484

Hom.:

29840

Bravo

AF:

0.453

Asia WGS

AF:

0.436

AC:

1517

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.25

(source)

DANN

Benign

0.48

PhyloP100

-0.35

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