Variant 8-17538871-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000004531.14(SLC7A2):c.47G>A(p.Arg16Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 1,609,622 control chromosomes in the GnomAD database, including 28,858 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 1904 hom., cov: 33)

Exomes 𝑓: 0.18 ( 26954 hom. )

Consequence

SLC7A2
ENST00000004531.14 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.795

Variant links:

Genes affected

SLC7A2 (HGNC:11060): (solute carrier family 7 member 2) The protein encoded by this gene is a cationic amino acid transporter and a member of the APC (amino acid-polyamine-organocation) family of transporters. The encoded membrane protein is responsible for the cellular uptake of arginine, lysine and ornithine. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

SLC7A2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0050296485).

BP6

Variant 8-17538871-G-A is Benign according to our data. Variant chr8-17538871-G-A is described in ClinVar as [Benign]. Clinvar id is 3059691.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC7A2	NM_001370338.1 linkuse as main transcript	c.-22-4447G>A		intron_variant		ENST00000494857.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC7A2	ENST00000494857.6 linkuse as main transcript	c.-22-4447G>A		intron_variant		5	NM_001370338.1	P4	P52569-1

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20650

AN:

152060

Hom.:

1904

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0364

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.102

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0499

Gnomad FIN

AF:

0.220

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.144

GnomAD3 exomes

AF:

0.141

AC:

35021

AN:

249204

Hom.:

3389

AF XY:

0.142

AC XY:

19163

AN XY:

135214

show subpopulations

Gnomad AFR exome

AF:

0.0310

Gnomad AMR exome

AF:

0.0781

Gnomad ASJ exome

AF:

0.173

Gnomad EAS exome

AF:

0.000556

Gnomad SAS exome

AF:

0.0519

Gnomad FIN exome

AF:

0.222

Gnomad NFE exome

AF:

0.201

Gnomad OTH exome

AF:

0.166

GnomAD4 exome

AF:

0.182

AC:

264710

AN:

1457444

Hom.:

26954

Cov.:

AF XY:

0.178

AC XY:

129403

AN XY:

725188

show subpopulations

Gnomad4 AFR exome

AF:

0.0297

Gnomad4 AMR exome

AF:

0.0832

Gnomad4 ASJ exome

AF:

0.174

Gnomad4 EAS exome

AF:

0.000479

Gnomad4 SAS exome

AF:

0.0533

Gnomad4 FIN exome

AF:

0.221

Gnomad4 NFE exome

AF:

0.207

Gnomad4 OTH exome

AF:

0.157

GnomAD4 genome

AF:

0.136

AC:

20654

AN:

152178

Hom.:

1904

Cov.:

AF XY:

0.133

AC XY:

9880

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.0363

Gnomad4 AMR

AF:

0.102

Gnomad4 ASJ

AF:

0.174

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.0508

Gnomad4 FIN

AF:

0.220

Gnomad4 NFE

AF:

0.206

Gnomad4 OTH

AF:

0.143

Alfa

AF:

0.182

Hom.:

4747

Bravo

AF:

0.123

TwinsUK

AF:

0.212

AC:

785

ALSPAC

AF:

0.209

AC:

805

ESP6500AA

AF:

0.0360

AC:

134

ESP6500EA

AF:

0.193

AC:

1578

ExAC

AF:

0.141

AC:

17062

Asia WGS

AF:

0.0310

AC:

109

AN:

3478

EpiCase

AF:

0.198

EpiControl

AF:

0.197

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

SLC7A2-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 01, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.47

CADD

Benign

6.4

DANN

Benign

0.96

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.072

MetaRNN

Benign

0.0027

T;T;T;T

MetaSVM

Benign

-0.98

MutationTaster

Benign

1.0

P;P;P;P;P

PrimateAI

Benign

0.21

PROVEAN

Benign

-0.030

N;N;N;.

REVEL

Benign

0.11

Sift

Pathogenic

0.0

D;D;D;.

Polyphen

0.0010

B;B;B;.

Vest4

0.086

MPC

0.022

ClinPred

0.0046

GERP RS

0.56

gMVP

0.19

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