Variant rs9693999 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_138817.3(SLC7A13):c.1408G>A(p.Glu470Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00642 in 1,596,532 control chromosomes in the GnomAD database, including 486 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.032 ( 270 hom., cov: 33)

Exomes 𝑓: 0.0038 ( 216 hom. )

Consequence

SLC7A13
NM_138817.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.71

Variant links:

Genes affected

SLC7A13 (HGNC:23092): (solute carrier family 7 member 13) Predicted to enable L-amino acid transmembrane transporter activity. Predicted to be involved in L-cystine transport; L-glutamate transmembrane transport; and aspartate transmembrane transport. Predicted to be integral component of membrane. Predicted to be active in apical plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC7A13 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017810166).

BP6

Variant 8-86214418-C-T is Benign according to our data. Variant chr8-86214418-C-T is described in ClinVar as [Benign]. Clinvar id is 1603156.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A13	NM_138817.3 linkuse as main transcript	c.1408G>A	p.Glu470Lys	missense_variant	4/4	ENST00000297524.8	NP_620172.2
SLC7A13	XM_011516867.3 linkuse as main transcript	c.1381G>A	p.Glu461Lys	missense_variant	4/4		XP_011515169.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC7A13	ENST00000297524.8 linkuse as main transcript	c.1408G>A	p.Glu470Lys	missense_variant	4/4	1	NM_138817.3	ENSP00000297524	P1	Q8TCU3-1
SLC7A13	ENST00000419776.2 linkuse as main transcript	c.*207G>A		3_prime_UTR_variant	5/5	1		ENSP00000410982		Q8TCU3-2

Frequencies

GnomAD3 genomes

AF:

0.0314

AC:

4780

AN:

152030

Hom.:

270

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.00330

Gnomad AMR

AF:

0.0138

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00767

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000573

Gnomad OTH

AF:

0.0239

GnomAD3 exomes

AF:

0.00896

AC:

2158

AN:

240772

Hom.:

103

AF XY:

0.00713

AC XY:

933

AN XY:

130942

show subpopulations

Gnomad AFR exome

AF:

0.110

Gnomad AMR exome

AF:

0.00570

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00581

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000370

Gnomad OTH exome

AF:

0.00441

GnomAD4 exome

AF:

0.00377

AC:

5443

AN:

1444384

Hom.:

216

Cov.:

AF XY:

0.00347

AC XY:

2497

AN XY:

719310

show subpopulations

Gnomad4 AFR exome

AF:

0.112

Gnomad4 AMR exome

AF:

0.00647

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000254

Gnomad4 SAS exome

AF:

0.00553

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000419

Gnomad4 OTH exome

AF:

0.00818

GnomAD4 genome

AF:

0.0316

AC:

4803

AN:

152148

Hom.:

270

Cov.:

AF XY:

0.0310

AC XY:

2304

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.107

Gnomad4 AMR

AF:

0.0138

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00767

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000574

Gnomad4 OTH

AF:

0.0265

Alfa

AF:

0.00542

Hom.:

Bravo

AF:

0.0352

ESP6500AA

AF:

0.0945

AC:

416

ESP6500EA

AF:

0.000698

AC:

ExAC

AF:

0.0106

AC:

1286

Asia WGS

AF:

0.0150

AC:

AN:

3476

EpiCase

AF:

0.000389

EpiControl

AF:

0.000482

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 25, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.089

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.38

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.025

Eigen

Benign

-0.84

Eigen_PC

Benign

-0.85

FATHMM_MKL

Benign

0.054

LIST_S2

Benign

0.60

MetaRNN

Benign

0.0018

MetaSVM

Benign

-0.97

MutationAssessor

Benign

1.4

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.47

PROVEAN

Benign

-1.6

REVEL

Benign

0.14

Sift

Benign

0.19

Sift4G

Uncertain

0.023

Polyphen

0.068

Vest4

0.10

MPC

0.0091

ClinPred

0.014

GERP RS

2.3

Varity_R

0.040

gMVP

0.35

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over