17-4938145-C-A
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.737+9G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000193 in 1,614,176 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000098 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00020 ( 5 hom. )
Consequence
SLC25A11
NM_003562.5 intron
NM_003562.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.28
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=-0.85).
BP6
Variant 17-4938145-C-A is Benign according to our data. Variant chr17-4938145-C-A is described in ClinVar as [Benign]. Clinvar id is 3711430.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 15 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A11 | NM_003562.5 | c.737+9G>T | intron_variant | Intron 6 of 7 | ENST00000225665.12 | NP_003553.2 | ||
SLC25A11 | NM_001165417.2 | c.704+9G>T | intron_variant | Intron 6 of 7 | NP_001158889.1 | |||
SLC25A11 | NM_001165418.2 | c.584+9G>T | intron_variant | Intron 5 of 6 | NP_001158890.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152248Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000398 AC: 100AN: 251188Hom.: 2 AF XY: 0.000589 AC XY: 80AN XY: 135750
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GnomAD4 exome AF: 0.000203 AC: 297AN: 1461810Hom.: 5 Cov.: 32 AF XY: 0.000294 AC XY: 214AN XY: 727216
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GnomAD4 genome AF: 0.0000984 AC: 15AN: 152366Hom.: 1 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74514
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Nov 06, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: 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
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