chr11-62882993-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001013251.3(SLC3A2):c.684G>A(p.Lys228=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000843 in 1,614,118 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.00048 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000043 ( 0 hom. )
Consequence
SLC3A2
NM_001013251.3 synonymous
NM_001013251.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.636
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 Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant 11-62882993-G-A is Benign according to our data. Variant chr11-62882993-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 722960.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.636 with no splicing effect.
BS2
High AC in GnomAd4 at 73 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC3A2 | NM_001013251.3 | c.684G>A | p.Lys228= | synonymous_variant | 3/9 | ENST00000338663.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC3A2 | ENST00000338663.12 | c.684G>A | p.Lys228= | synonymous_variant | 3/9 | 1 | NM_001013251.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000486 AC: 74AN: 152218Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000151 AC: 38AN: 251478Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135918
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GnomAD4 exome AF: 0.0000431 AC: 63AN: 1461782Hom.: 0 Cov.: 30 AF XY: 0.0000344 AC XY: 25AN XY: 727202
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GnomAD4 genome AF: 0.000479 AC: 73AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.000483 AC XY: 36AN XY: 74496
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at