Variant 14-22776092-T-C 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_003982.4(SLC7A7):c.894+103A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 1,523,346 control chromosomes in the GnomAD database, including 322,387 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.55 ( 25895 hom., cov: 31)

Exomes 𝑓: 0.65 ( 296492 hom. )

Consequence

SLC7A7
NM_003982.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.142

Variant links:

Genes affected

SLC7A7 (HGNC:11065): (solute carrier family 7 member 7) The protein encoded by this gene is the light subunit of a cationic amino acid transporter. This sodium-independent transporter is formed when the light subunit encoded by this gene dimerizes with the heavy subunit transporter protein SLC3A2. This transporter is found in epithelial cell membranes where it transfers cationic and large neutral amino acids from the cell to the extracellular space. Defects in this gene are a cause of lysinuric protein intolerance (LPI). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2011]

SLC7A7 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 (BayesDel_noAF=-0.82).

BP6

Variant 14-22776092-T-C is Benign according to our data. Variant chr14-22776092-T-C is described in ClinVar as [Benign]. Clinvar id is 1292095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-22776092-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC7A7	NM_003982.4 linkuse as main transcript	c.894+103A>G		intron_variant		ENST00000674313.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC7A7	ENST00000674313.1 linkuse as main transcript	c.894+103A>G		intron_variant			NM_003982.4	P1

Frequencies

GnomAD3 genomes

AF:

0.549

AC:

83375

AN:

151870

Hom.:

25881

Cov.:

show subpopulations

Gnomad AFR

AF:

0.230

Gnomad AMI

AF:

0.571

Gnomad AMR

AF:

0.704

Gnomad ASJ

AF:

0.697

Gnomad EAS

AF:

0.819

Gnomad SAS

AF:

0.668

Gnomad FIN

AF:

0.613

Gnomad MID

AF:

0.677

Gnomad NFE

AF:

0.659

Gnomad OTH

AF:

0.595

GnomAD4 exome

AF:

0.652

AC:

893723

AN:

1371358

Hom.:

296492

Cov.:

AF XY:

0.654

AC XY:

449277

AN XY:

687224

show subpopulations

Gnomad4 AFR exome

AF:

0.212

Gnomad4 AMR exome

AF:

0.783

Gnomad4 ASJ exome

AF:

0.701

Gnomad4 EAS exome

AF:

0.816

Gnomad4 SAS exome

AF:

0.669

Gnomad4 FIN exome

AF:

0.625

Gnomad4 NFE exome

AF:

0.652

Gnomad4 OTH exome

AF:

0.651

GnomAD4 genome

AF:

0.549

AC:

83398

AN:

151988

Hom.:

25895

Cov.:

AF XY:

0.553

AC XY:

41071

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.230

Gnomad4 AMR

AF:

0.705

Gnomad4 ASJ

AF:

0.697

Gnomad4 EAS

AF:

0.819

Gnomad4 SAS

AF:

0.669

Gnomad4 FIN

AF:

0.613

Gnomad4 NFE

AF:

0.659

Gnomad4 OTH

AF:

0.596

Alfa

AF:

0.641

Hom.:

46338

Bravo

AF:

0.543

Asia WGS

AF:

0.722

AC:

2511

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 77% of patients studied by a panel of primary immunodeficiencies. Number of patients: 73. Only high quality variants are reported. -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.2

DANN

Benign

0.79

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