Variant rs42139 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_002594.1(SLC7A5P2):n.157G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.50 ( 1205 hom., cov: 66)

Exomes 𝑓: 0.49 ( 6873 hom. )

Failed GnomAD Quality Control

Consequence

SLC7A5P2
NR_002594.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0270

Variant links:

Genes affected

(HGNC:):

links:

SLC7A5P2 (HGNC:24951): (solute carrier family 7 member 5 pseudogene 2) Predicted to enable L-amino acid transmembrane transporter activity. Predicted to be involved in L-alpha-amino acid transmembrane transport and L-amino acid transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC7A5P2 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC7A5P2	NR_002594.1 linkuse as main transcript	n.157G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000522841.6 linkuse as main transcript	n.157G>A		non_coding_transcript_exon_variant	1/12	2
SLC7A5P2	ENST00000553010.2 linkuse as main transcript	n.78G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

74331

AN:

149802

Hom.:

1197

Cov.:

FAILED QC

Gnomad AFR

AF:

0.507

Gnomad AMI

AF:

0.490

Gnomad AMR

AF:

0.507

Gnomad ASJ

AF:

0.497

Gnomad EAS

AF:

0.545

Gnomad SAS

AF:

0.486

Gnomad FIN

AF:

0.490

Gnomad MID

AF:

0.467

Gnomad NFE

AF:

0.485

Gnomad OTH

AF:

0.498

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.491

AC:

694847

AN:

1414702

Hom.:

6873

Cov.:

AF XY:

0.491

AC XY:

345596

AN XY:

704298

show subpopulations

Gnomad4 AFR exome

AF:

0.509

Gnomad4 AMR exome

AF:

0.543

Gnomad4 ASJ exome

AF:

0.497

Gnomad4 EAS exome

AF:

0.561

Gnomad4 SAS exome

AF:

0.484

Gnomad4 FIN exome

AF:

0.488

Gnomad4 NFE exome

AF:

0.487

Gnomad4 OTH exome

AF:

0.492

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.496

AC:

74402

AN:

149924

Hom.:

1205

Cov.:

AF XY:

0.497

AC XY:

36414

AN XY:

73242

show subpopulations

Gnomad4 AFR

AF:

0.507

Gnomad4 AMR

AF:

0.508

Gnomad4 ASJ

AF:

0.497

Gnomad4 EAS

AF:

0.545

Gnomad4 SAS

AF:

0.486

Gnomad4 FIN

AF:

0.490

Gnomad4 NFE

AF:

0.485

Gnomad4 OTH

AF:

0.497

Alfa

AF:

0.492

Hom.:

138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

Cadd

Benign

Dann

Benign

0.92

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.1

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over