Genetic Variant SLC7A2:c.-22-4388_-22-4387insC (chr8-17538930-T-TC) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_001370338.1(SLC7A2):c.-22-4388_-22-4387insC 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 1,611,760 control chromosomes in the GnomAD database, including 556 homozygotes. 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

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.823

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 -9 ACMG points.

BP6

Variant 8-17538930-T-TC is Benign according to our data. Variant chr8-17538930-T-TC is described in ClinVar as [Benign]. Clinvar id is 3059505.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC7A2	NM_001370338.1 link	c.-22-4388_-22-4387insC		intron_variant	Intron 2 of 12	ENST00000494857.6	NP_001357267.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC7A2	ENST00000494857.6 link	c.-22-4388_-22-4387insC		intron_variant	Intron 2 of 12	5	NM_001370338.1	ENSP00000419140.2		P52569-1

Frequencies

GnomAD3 genomes

AF:

0.0255

AC:

3884

AN:

152122

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:

0.0885

Gnomad SAS

AF:

0.0470

Gnomad FIN

AF:

0.0393

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00132

Gnomad OTH

AF:

0.0239

GnomAD3 exomes

AF:

0.0269

AC:

6695

AN:

249216

Hom.:

197

AF XY:

0.0251

AC XY:

3393

AN XY:

135208

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:

14522

AN:

1459520

Hom.:

451

Cov.:

AF XY:

0.0105

AC XY:

7614

AN XY:

726268

show subpopulations

Gnomad4 AFR exome

AF:

0.0496

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:

0.0255

AC:

3888

AN:

152240

Hom.:

105

Cov.:

AF XY:

0.0282

AC XY:

2099

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.0493

Gnomad4 AMR

AF:

0.0389

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0889

Gnomad4 SAS

AF:

0.0464

Gnomad4 FIN

AF:

0.0393

Gnomad4 NFE

AF:

0.00132

Gnomad4 OTH

AF:

0.0260

Alfa

AF:

0.00919

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

Nov 26, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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