Variant rs164365 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_145913.5(SLC5A8):c.1470G>T(p.Met490Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 1,612,632 control chromosomes in the GnomAD database, including 42,207 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict 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 ( 3819 hom., cov: 32)

Exomes 𝑓: 0.22 ( 38388 hom. )

Consequence

SLC5A8
NM_145913.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.241

Variant links:

Genes affected

SLC5A8 (HGNC:19119): (solute carrier family 5 member 8) SLC5A8 has been shown to transport iodide by a passive mechanism (Rodriguez et al., 2002 [PubMed 12107270]) and monocarboxylates and short-chain fatty acids by a sodium-coupled mechanism (Gopal et al., 2004 [PubMed 15322102]). In kidney, SLC5A8 functions as a high-affinity sodium-coupled lactate transporter involved in reabsorption of lactate and maintenance of blood lactate levels (Thangaraju et al., 2006 [PubMed 16873376]).[supplied by OMIM, Dec 2008]

SLC5A8 links:

SLC5A8 (HGNC:):

SLC5A8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=8.911971E-5).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC5A8	NM_145913.5 linkuse as main transcript	c.1470G>T	p.Met490Ile	missense_variant	12/15	ENST00000536262.3	NP_666018.3	Q8N695
SLC5A8	XR_007063055.1 linkuse as main transcript	n.1860G>T		non_coding_transcript_exon_variant	12/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC5A8	ENST00000536262.3 linkuse as main transcript	c.1470G>T	p.Met490Ile	missense_variant	12/15	1	NM_145913.5	ENSP00000445340.2		Q8N695

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31659

AN:

151896

Hom.:

3823

Cov.:

show subpopulations

Gnomad AFR

AF:

0.138

Gnomad AMI

AF:

0.237

Gnomad AMR

AF:

0.170

Gnomad ASJ

AF:

0.279

Gnomad EAS

AF:

0.528

Gnomad SAS

AF:

0.227

Gnomad FIN

AF:

0.314

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.213

Gnomad OTH

AF:

0.218

GnomAD3 exomes

AF:

0.234

AC:

58529

AN:

250660

Hom.:

8255

AF XY:

0.235

AC XY:

31903

AN XY:

135488

show subpopulations

Gnomad AFR exome

AF:

0.141

Gnomad AMR exome

AF:

0.123

Gnomad ASJ exome

AF:

0.269

Gnomad EAS exome

AF:

0.551

Gnomad SAS exome

AF:

0.214

Gnomad FIN exome

AF:

0.312

Gnomad NFE exome

AF:

0.216

Gnomad OTH exome

AF:

0.230

GnomAD4 exome

AF:

0.220

AC:

322031

AN:

1460618

Hom.:

38388

Cov.:

AF XY:

0.222

AC XY:

160998

AN XY:

726614

show subpopulations

Gnomad4 AFR exome

AF:

0.135

Gnomad4 AMR exome

AF:

0.128

Gnomad4 ASJ exome

AF:

0.275

Gnomad4 EAS exome

AF:

0.524

Gnomad4 SAS exome

AF:

0.220

Gnomad4 FIN exome

AF:

0.303

Gnomad4 NFE exome

AF:

0.210

Gnomad4 OTH exome

AF:

0.233

GnomAD4 genome

AF:

0.208

AC:

31648

AN:

152014

Hom.:

3819

Cov.:

AF XY:

0.216

AC XY:

16029

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.138

Gnomad4 AMR

AF:

0.169

Gnomad4 ASJ

AF:

0.279

Gnomad4 EAS

AF:

0.528

Gnomad4 SAS

AF:

0.227

Gnomad4 FIN

AF:

0.314

Gnomad4 NFE

AF:

0.213

Gnomad4 OTH

AF:

0.218

Alfa

AF:

0.219

Hom.:

7864

Bravo

AF:

0.198

TwinsUK

AF:

0.198

AC:

733

ALSPAC

AF:

0.206

AC:

793

ESP6500AA

AF:

0.135

AC:

597

ESP6500EA

AF:

0.225

AC:

1932

ExAC

AF:

0.234

AC:

28443

Asia WGS

AF:

0.312

AC:

1084

AN:

3478

EpiCase

AF:

0.227

EpiControl

AF:

0.225

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.57

CADD

Benign

5.1

DANN

Benign

0.44

DEOGEN2

Benign

0.042

Eigen

Benign

-0.64

Eigen_PC

Benign

-0.57

FATHMM_MKL

Benign

0.026

MetaRNN

Benign

0.000089

MetaSVM

Benign

-0.90

MutationAssessor

Benign

1.7

PrimateAI

Benign

0.28

PROVEAN

Benign

-0.26

REVEL

Benign

0.099

Sift

Benign

0.43

Sift4G

Benign

0.43

Polyphen

0.0020

Vest4

0.039

MutPred

0.39

Loss of sheet (P = 0.0315);

MPC

0.12

ClinPred

0.0069

GERP RS

3.0

Varity_R

0.11

gMVP

0.54

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over