17-4937837-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003562.5(SLC25A11):c.849G>A(p.Thr283Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,614,114 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00061 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 2 hom. )
Consequence
SLC25A11
NM_003562.5 synonymous
NM_003562.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.95
Genes affected
SLC25A11 (HGNC:10981): (solute carrier family 25 member 11) The oxoglutarate/malate carrier transports 2-oxoglutarate across the inner membranes of mitochondria in an electroneutral exchange for malate or other dicarboxylic acids (summary by Iacobazzi et al., 1992 [PubMed 1457818]).[supplied by OMIM, Jan 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 17-4937837-C-T is Benign according to our data. Variant chr17-4937837-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2753197.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 93 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A11 | NM_003562.5 | c.849G>A | p.Thr283Thr | synonymous_variant | Exon 8 of 8 | ENST00000225665.12 | NP_003553.2 | |
SLC25A11 | NM_001165417.2 | c.816G>A | p.Thr272Thr | synonymous_variant | Exon 8 of 8 | NP_001158889.1 | ||
SLC25A11 | NM_001165418.2 | c.696G>A | p.Thr232Thr | synonymous_variant | Exon 7 of 7 | NP_001158890.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A11 | ENST00000225665.12 | c.849G>A | p.Thr283Thr | synonymous_variant | Exon 8 of 8 | 1 | NM_003562.5 | ENSP00000225665.7 | ||
SLC25A11 | ENST00000576951.1 | c.816G>A | p.Thr272Thr | synonymous_variant | Exon 8 of 8 | 5 | ENSP00000458993.1 | |||
SLC25A11 | ENST00000544061.6 | c.696G>A | p.Thr232Thr | synonymous_variant | Exon 7 of 7 | 3 | ENSP00000440804.2 | |||
SLC25A11 | ENST00000574710.1 | n.1656G>A | non_coding_transcript_exon_variant | Exon 6 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000611 AC: 93AN: 152198Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000617 AC: 155AN: 251018Hom.: 0 AF XY: 0.000516 AC XY: 70AN XY: 135670
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GnomAD4 exome AF: 0.00106 AC: 1554AN: 1461798Hom.: 2 Cov.: 32 AF XY: 0.00105 AC XY: 761AN XY: 727202
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GnomAD4 genome AF: 0.000611 AC: 93AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.000577 AC XY: 43AN XY: 74480
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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
Oct 02, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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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