Genetic Variant SLC3A2:c.299-226C>T (chr11-62880793-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000377890.6(SLC3A2):c.299-226C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SLC3A2
ENST00000377890.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.411

Publications

2 publications found

Variant links:

Genes affected

SLC3A2 (HGNC:11026): (solute carrier family 3 member 2) This gene is a member of the solute carrier family and encodes a cell surface, transmembrane protein. The protein exists as the heavy chain of a heterodimer, covalently bound through di-sulfide bonds to one of several possible light chains. The encoded transporter plays a role in regulation of intracellular calcium levels and transports L-type amino acids. Alternatively spliced transcript variants, encoding different isoforms, have been characterized. [provided by RefSeq, Nov 2010]

SLC3A2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
SLC3A2	NM_001012662.3 link	c.302-226C>T	intron_variant	Intron 3 of 11		NP_001012680.1
SLC3A2	NM_002394.6 link	c.299-226C>T	intron_variant	Intron 3 of 11		NP_002385.3
SLC3A2	NM_001012664.3 link	c.113-226C>T	intron_variant	Intron 1 of 9		NP_001012682.1
SLC3A2	NM_001013251.3 link	c.-231C>T	upstream_gene_variant		ENST00000338663.12	NP_001013269.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC3A2	ENST00000338663.12 link	c.-231C>T		upstream_gene_variant		1	NM_001013251.3	ENSP00000340815.7

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

673486

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

338410

African (AFR)

AF:

0.00

AC:

AN:

16374

American (AMR)

AF:

0.00

AC:

AN:

14918

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14466

East Asian (EAS)

AF:

0.00

AC:

AN:

29598

South Asian (SAS)

AF:

0.00

AC:

AN:

42832

European-Finnish (FIN)

AF:

0.00

AC:

AN:

28380

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2398

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

491820

Other (OTH)

AF:

0.00

AC:

AN:

32700

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

2.1

(source)

DANN

Benign

0.83

PhyloP100

-0.41

PromoterAI

-0.26

Neutral

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over