chr22-19176063-T-TCA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_005984.5(SLC25A1):c.*66_*67insTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00826 in 947,492 control chromosomes in the GnomAD database, including 55 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.013 ( 2 hom., cov: 34)
Exomes 𝑓: 0.0079 ( 53 hom. )
Consequence
SLC25A1
NM_005984.5 3_prime_UTR
NM_005984.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.466
Genes affected
SLC25A1 (HGNC:10979): (solute carrier family 25 member 1) This gene encodes a member of the mitochondrial carrier subfamily of solute carrier proteins. Members of this family include nuclear-encoded transporters that translocate small metabolites across the mitochondrial membrane. This protein regulates the movement of citrate across the inner membranes of the mitochondria. Mutations in this gene have been associated with combined D-2- and L-2-hydroxyglutaric aciduria. Pseudogenes of this gene have been identified on chromosomes 7, 11, 16, and 19. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 22-19176063-T-TCA is Benign according to our data. Variant chr22-19176063-T-TCA is described in ClinVar as [Likely_benign]. Clinvar id is 1327332.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0133 (839/62976) while in subpopulation AMR AF= 0.0126 (80/6336). AF 95% confidence interval is 0.0104. There are 2 homozygotes in gnomad4. There are 448 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A1 | NM_005984.5 | c.*66_*67insTG | 3_prime_UTR_variant | 9/9 | ENST00000215882.10 | ||
SLC25A1 | NM_001256534.2 | c.*66_*67insTG | 3_prime_UTR_variant | 8/8 | |||
SLC25A1 | NM_001287387.2 | c.*66_*67insTG | 3_prime_UTR_variant | 9/9 | |||
SLC25A1 | NR_046298.3 | n.926_927insTG | non_coding_transcript_exon_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A1 | ENST00000215882.10 | c.*66_*67insTG | 3_prime_UTR_variant | 9/9 | 1 | NM_005984.5 | P1 | ||
SLC25A1 | ENST00000451283.5 | c.*66_*67insTG | 3_prime_UTR_variant | 9/9 | 2 | ||||
SLC25A1 | ENST00000470922.5 | n.1144_1145insTG | non_coding_transcript_exon_variant | 8/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0133 AC: 839AN: 63002Hom.: 2 Cov.: 34
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GnomAD4 exome AF: 0.00790 AC: 6990AN: 884516Hom.: 53 Cov.: 16 AF XY: 0.00789 AC XY: 3593AN XY: 455184
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GnomAD4 genome ? AF: 0.0133 AC: 839AN: 62976Hom.: 2 Cov.: 34 AF XY: 0.0148 AC XY: 448AN XY: 30206
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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 | GeneDx | Jun 01, 2021 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at