chr11-62876814-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000377890.6(SLC3A2):c.299-4205C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000284 in 597,626 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000020 ( 0 hom. )
Consequence
SLC3A2
ENST00000377890.6 intron
ENST00000377890.6 intron
Scores
3
12
Clinical Significance
Conservation
PhyloP100: 0.0700
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.08749357).
BS2
?
High AC in GnomAd at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC3A2 | NM_001012662.3 | c.236C>A | p.Ala79Asp | missense_variant | 3/12 | ||
SLC3A2 | NM_001012664.3 | c.113-4205C>A | intron_variant | ||||
SLC3A2 | NM_002394.6 | c.299-4205C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC3A2 | ENST00000377889.6 | c.113-4205C>A | intron_variant | 1 | |||||
SLC3A2 | ENST00000377890.6 | c.299-4205C>A | intron_variant | 1 | |||||
SLC3A2 | ENST00000538084.2 | c.326C>A | p.Ala109Asp | missense_variant | 4/13 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152048Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000202 AC: 9AN: 445578Hom.: 0 Cov.: 7 AF XY: 0.0000307 AC XY: 7AN XY: 228094
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GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152048Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74262
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2022 | The c.236C>A (p.A79D) alteration is located in exon 3 (coding exon 3) of the SLC3A2 gene. This alteration results from a C to A substitution at nucleotide position 236, causing the alanine (A) at amino acid position 79 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at