Variant 5-139379813-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_005847.5(SLC23A1):c.790G>A(p.Val264Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0315 in 1,613,960 control chromosomes in the GnomAD database, including 952 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.039 ( 159 hom., cov: 32)

Exomes 𝑓: 0.031 ( 793 hom. )

Consequence

SLC23A1
NM_005847.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.17

Variant links:

Genes affected

SLC23A1 (HGNC:10974): (solute carrier family 23 member 1) The absorption of vitamin C into the body and its distribution to organs requires two sodium-dependent vitamin C transporters. This gene encodes one of the two transporters. The encoded protein is active in bulk vitamin C transport involving epithelial surfaces. Previously, this gene had an official symbol of SLC23A2. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

SLC23A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0032784939).

BP6

Variant 5-139379813-C-T is Benign according to our data. Variant chr5-139379813-C-T is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC23A1	NM_005847.5 linkuse as main transcript	c.790G>A	p.Val264Met	missense_variant	8/15	ENST00000348729.8	NP_005838.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC23A1	ENST00000348729.8 linkuse as main transcript	c.790G>A	p.Val264Met	missense_variant	8/15	1	NM_005847.5	ENSP00000302701	P1	Q9UHI7-1
SLC23A1	ENST00000353963.7 linkuse as main transcript	c.802G>A	p.Val268Met	missense_variant	8/15	1		ENSP00000302851		Q9UHI7-2
SLC23A1	ENST00000504513.1 linkuse as main transcript	c.164+143G>A		intron_variant		5		ENSP00000422688
SLC23A1	ENST00000506512.1 linkuse as main transcript	n.401G>A		non_coding_transcript_exon_variant	1/2	4

Frequencies

GnomAD3 genomes

AF:

0.0391

AC:

5937

AN:

151984

Hom.:

160

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0724

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0263

Gnomad ASJ

AF:

0.00893

Gnomad EAS

AF:

0.0164

Gnomad SAS

AF:

0.0166

Gnomad FIN

AF:

0.0256

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0295

Gnomad OTH

AF:

0.0326

GnomAD3 exomes

AF:

0.0273

AC:

6863

AN:

251368

Hom.:

135

AF XY:

0.0265

AC XY:

3595

AN XY:

135854

show subpopulations

Gnomad AFR exome

AF:

0.0669

Gnomad AMR exome

AF:

0.0182

Gnomad ASJ exome

AF:

0.0108

Gnomad EAS exome

AF:

0.0168

Gnomad SAS exome

AF:

0.0167

Gnomad FIN exome

AF:

0.0219

Gnomad NFE exome

AF:

0.0318

Gnomad OTH exome

AF:

0.0217

GnomAD4 exome

AF:

0.0307

AC:

44905

AN:

1461858

Hom.:

793

Cov.:

AF XY:

0.0299

AC XY:

21748

AN XY:

727236

show subpopulations

Gnomad4 AFR exome

AF:

0.0689

Gnomad4 AMR exome

AF:

0.0194

Gnomad4 ASJ exome

AF:

0.00953

Gnomad4 EAS exome

AF:

0.00962

Gnomad4 SAS exome

AF:

0.0168

Gnomad4 FIN exome

AF:

0.0223

Gnomad4 NFE exome

AF:

0.0329

Gnomad4 OTH exome

AF:

0.0305

GnomAD4 genome

AF:

0.0391

AC:

5944

AN:

152102

Hom.:

159

Cov.:

AF XY:

0.0380

AC XY:

2828

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.0723

Gnomad4 AMR

AF:

0.0264

Gnomad4 ASJ

AF:

0.00893

Gnomad4 EAS

AF:

0.0164

Gnomad4 SAS

AF:

0.0168

Gnomad4 FIN

AF:

0.0256

Gnomad4 NFE

AF:

0.0295

Gnomad4 OTH

AF:

0.0327

Alfa

AF:

0.0279

Hom.:

128

Bravo

AF:

0.0414

TwinsUK

AF:

0.0351

AC:

130

ALSPAC

AF:

0.0324

AC:

125

ESP6500AA

AF:

0.0649

AC:

286

ESP6500EA

AF:

0.0345

AC:

297

ExAC

AF:

0.0294

AC:

3566

Asia WGS

AF:

0.0240

AC:

AN:

3478

EpiCase

AF:

0.0289

EpiControl

AF:

0.0280

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Uncertain

1.0

Eigen

Benign

-0.19

Eigen_PC

Benign

-0.21

FATHMM_MKL

Uncertain

0.83

MetaRNN

Benign

0.0033

T;T

MetaSVM

Benign

-1.2

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.59

PROVEAN

Benign

-0.59

N;N

REVEL

Benign

0.065

Sift

Benign

0.19

T;T

Sift4G

Benign

0.14

T;T

Vest4

0.093

MPC

0.82

ClinPred

0.016

GERP RS

2.7

gMVP

0.88

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

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