Variant 8-17538906-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM1BP4_StrongBP6BA1

The NM_001164771.2(SLC7A2):c.82G>C(p.Asp28His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 1,606,984 control chromosomes in the GnomAD database, including 37,478 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 (no stars).

Frequency

Genomes: 𝑓 0.22 ( 4077 hom., cov: 32)

Exomes 𝑓: 0.21 ( 33401 hom. )

Consequence

SLC7A2
NM_001164771.2 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.0660

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

PM1

In a modified_residue Phosphothreonine (size 0) in uniprot entity CTR2_HUMAN

BP4

Computational evidence support a benign effect (MetaRNN=0.004436016).

BP6

Variant 8-17538906-G-C is Benign according to our data. Variant chr8-17538906-G-C is described in ClinVar as [Benign]. Clinvar id is 3059575.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A2	NM_001370338.1 linkuse as main transcript	c.-22-4412G>C		intron_variant		ENST00000494857.6	NP_001357267.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC7A2	ENST00000494857.6 linkuse as main transcript	c.-22-4412G>C		intron_variant		5	NM_001370338.1	ENSP00000419140.2		P52569-1

Frequencies

GnomAD3 genomes

AF:

0.225

AC:

34152

AN:

151878

Hom.:

4075

Cov.:

show subpopulations

Gnomad AFR

AF:

0.288

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.162

Gnomad ASJ

AF:

0.184

Gnomad EAS

AF:

0.107

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.227

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.220

Gnomad OTH

AF:

0.213

GnomAD3 exomes

AF:

0.191

AC:

47619

AN:

249004

Hom.:

5058

AF XY:

0.188

AC XY:

25390

AN XY:

135106

show subpopulations

Gnomad AFR exome

AF:

0.291

Gnomad AMR exome

AF:

0.151

Gnomad ASJ exome

AF:

0.180

Gnomad EAS exome

AF:

0.111

Gnomad SAS exome

AF:

0.117

Gnomad FIN exome

AF:

0.232

Gnomad NFE exome

AF:

0.215

Gnomad OTH exome

AF:

0.200

GnomAD4 exome

AF:

0.209

AC:

304812

AN:

1454988

Hom.:

33401

Cov.:

AF XY:

0.207

AC XY:

149531

AN XY:

724098

show subpopulations

Gnomad4 AFR exome

AF:

0.290

Gnomad4 AMR exome

AF:

0.155

Gnomad4 ASJ exome

AF:

0.181

Gnomad4 EAS exome

AF:

0.128

Gnomad4 SAS exome

AF:

0.121

Gnomad4 FIN exome

AF:

0.231

Gnomad4 NFE exome

AF:

0.220

Gnomad4 OTH exome

AF:

0.198

GnomAD4 genome

AF:

0.225

AC:

34166

AN:

151996

Hom.:

4077

Cov.:

AF XY:

0.220

AC XY:

16365

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.288

Gnomad4 AMR

AF:

0.162

Gnomad4 ASJ

AF:

0.184

Gnomad4 EAS

AF:

0.107

Gnomad4 SAS

AF:

0.124

Gnomad4 FIN

AF:

0.227

Gnomad4 NFE

AF:

0.220

Gnomad4 OTH

AF:

0.211

Alfa

AF:

0.158

Hom.:

459

Bravo

AF:

0.228

TwinsUK

AF:

0.222

AC:

822

ALSPAC

AF:

0.222

AC:

857

ESP6500AA

AF:

0.276

AC:

1012

ESP6500EA

AF:

0.211

AC:

1725

ExAC

AF:

0.195

AC:

23571

EpiCase

AF:

0.214

EpiControl

AF:

0.215

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SLC7A2-related disorder

Benign:1

Benign, no assertion criteria provided

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

-0.63

BayesDel_noAF

Benign

-0.53

CADD

Benign

1.9

DANN

Benign

0.65

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.0036

LIST_S2

Benign

0.25

.;T;T;T

MetaRNN

Benign

0.0044

T;T;T;T

MetaSVM

Benign

-1.1

PrimateAI

Benign

0.26

PROVEAN

Benign

-0.25

N;N;N;.

REVEL

Benign

0.12

Sift

Benign

0.070

T;T;T;.

Sift4G

Uncertain

0.037

D;D;D;.

Polyphen

0.0

B;B;B;.

Vest4

0.054

MPC

0.022

ClinPred

0.0014

GERP RS

-1.8

gMVP

0.27

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