Variant chr8-17538932-A-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001370338.1(SLC7A2):c.-22-4386A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0114 in 1,611,186 control chromosomes in the GnomAD database, including 556 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.026 ( 105 hom., cov: 32)

Exomes 𝑓: 0.0099 ( 451 hom. )

Consequence

SLC7A2
NM_001370338.1 intron

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.455

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 8-17538932-A-C is Benign according to our data. Variant chr8-17538932-A-C is described in ClinVar as [Benign]. Clinvar id is 3058848.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0825 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.-22-4386A>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.-22-4386A>C		intron_variant		5	NM_001370338.1	ENSP00000419140.2		P52569-1

Frequencies

GnomAD3 genomes

AF:

0.0255

AC:

3886

AN:

152118

Hom.:

104

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0494

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0390

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0888

Gnomad SAS

AF:

0.0470

Gnomad FIN

AF:

0.0392

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00132

Gnomad OTH

AF:

0.0239

GnomAD3 exomes

AF:

0.0269

AC:

6696

AN:

249278

Hom.:

196

AF XY:

0.0251

AC XY:

3393

AN XY:

135246

show subpopulations

Gnomad AFR exome

AF:

0.0491

Gnomad AMR exome

AF:

0.0643

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0789

Gnomad SAS exome

AF:

0.0391

Gnomad FIN exome

AF:

0.0362

Gnomad NFE exome

AF:

0.00186

Gnomad OTH exome

AF:

0.0194

GnomAD4 exome

AF:

0.00995

AC:

14514

AN:

1458950

Hom.:

451

Cov.:

AF XY:

0.0105

AC XY:

7608

AN XY:

725990

show subpopulations

Gnomad4 AFR exome

AF:

0.0495

Gnomad4 AMR exome

AF:

0.0613

Gnomad4 ASJ exome

AF:

0.0000766

Gnomad4 EAS exome

AF:

0.0896

Gnomad4 SAS exome

AF:

0.0368

Gnomad4 FIN exome

AF:

0.0324

Gnomad4 NFE exome

AF:

0.000665

Gnomad4 OTH exome

AF:

0.0149

GnomAD4 genome

AF:

0.0256

AC:

3890

AN:

152236

Hom.:

105

Cov.:

AF XY:

0.0282

AC XY:

2100

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.0493

Gnomad4 AMR

AF:

0.0388

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0892

Gnomad4 SAS

AF:

0.0464

Gnomad4 FIN

AF:

0.0392

Gnomad4 NFE

AF:

0.00132

Gnomad4 OTH

AF:

0.0261

Alfa

AF:

0.00760

Hom.:

Bravo

AF:

0.0265

Asia WGS

AF:

0.0640

AC:

222

AN:

3478

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 26, 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_noAF

Benign

-0.66

CADD

Benign

8.5

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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