Variant 8-86214471-A-G 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.1355T>C(p.Met452Thr) variant causes a missense change. The variant allele was found at a frequency of 0.107 in 1,610,534 control chromosomes in the GnomAD database, including 11,325 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 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 0.14 ( 1729 hom., cov: 32)

Exomes 𝑓: 0.10 ( 9596 hom. )

Consequence

SLC7A13
NM_138817.3 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 3.66

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0023793578).

BP6

Variant 8-86214471-A-G is Benign according to our data. Variant chr8-86214471-A-G is described in ClinVar as [Benign]. Clinvar id is 1598705.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.203 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.1355T>C	p.Met452Thr	missense_variant	4/4	ENST00000297524.8	NP_620172.2	Q8TCU3-1
SLC7A13	XM_011516867.3 linkuse as main transcript	c.1328T>C	p.Met443Thr	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.1355T>C	p.Met452Thr	missense_variant	4/4	1	NM_138817.3	ENSP00000297524.3		Q8TCU3-1
SLC7A13	ENST00000419776.2 linkuse as main transcript	c.*154T>C		3_prime_UTR_variant	5/5	1		ENSP00000410982.2		Q8TCU3-2

Frequencies

GnomAD3 genomes

AF:

0.137

AC:

20812

AN:

152070

Hom.:

1719

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.0956

Gnomad AMR

AF:

0.208

Gnomad ASJ

AF:

0.0496

Gnomad EAS

AF:

0.136

Gnomad SAS

AF:

0.173

Gnomad FIN

AF:

0.171

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0916

Gnomad OTH

AF:

0.132

GnomAD3 exomes

AF:

0.140

AC:

34902

AN:

249304

Hom.:

3181

AF XY:

0.134

AC XY:

18049

AN XY:

134944

show subpopulations

Gnomad AFR exome

AF:

0.183

Gnomad AMR exome

AF:

0.275

Gnomad ASJ exome

AF:

0.0523

Gnomad EAS exome

AF:

0.138

Gnomad SAS exome

AF:

0.162

Gnomad FIN exome

AF:

0.169

Gnomad NFE exome

AF:

0.0910

Gnomad OTH exome

AF:

0.118

GnomAD4 exome

AF:

0.104

AC:

151476

AN:

1458346

Hom.:

9596

Cov.:

AF XY:

0.105

AC XY:

76232

AN XY:

725622

show subpopulations

Gnomad4 AFR exome

AF:

0.191

Gnomad4 AMR exome

AF:

0.268

Gnomad4 ASJ exome

AF:

0.0528

Gnomad4 EAS exome

AF:

0.163

Gnomad4 SAS exome

AF:

0.160

Gnomad4 FIN exome

AF:

0.173

Gnomad4 NFE exome

AF:

0.0858

Gnomad4 OTH exome

AF:

0.109

GnomAD4 genome

AF:

0.137

AC:

20845

AN:

152188

Hom.:

1729

Cov.:

AF XY:

0.143

AC XY:

10656

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.181

Gnomad4 AMR

AF:

0.209

Gnomad4 ASJ

AF:

0.0496

Gnomad4 EAS

AF:

0.136

Gnomad4 SAS

AF:

0.172

Gnomad4 FIN

AF:

0.171

Gnomad4 NFE

AF:

0.0916

Gnomad4 OTH

AF:

0.135

Alfa

AF:

0.0961

Hom.:

1970

Bravo

AF:

0.142

TwinsUK

AF:

0.0769

AC:

285

ALSPAC

AF:

0.0856

AC:

330

ESP6500AA

AF:

0.174

AC:

768

ESP6500EA

AF:

0.0906

AC:

779

ExAC

AF:

0.136

AC:

16448

Asia WGS

AF:

0.141

AC:

488

AN:

3474

EpiCase

AF:

0.0889

EpiControl

AF:

0.0838

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 29, 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

0.18

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.35

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.023

Eigen

Benign

-0.56

Eigen_PC

Benign

-0.45

FATHMM_MKL

Benign

0.49

LIST_S2

Benign

0.47

MetaRNN

Benign

0.0024

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.34

PrimateAI

Benign

0.47

PROVEAN

Benign

-2.0

REVEL

Benign

0.16

Sift

Uncertain

0.0040

Sift4G

Benign

0.22

Polyphen

0.039

Vest4

0.080

MPC

0.0095

ClinPred

0.042

GERP RS

4.2

Varity_R

0.40

gMVP

0.29

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