chr5-110738678-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001303250.3(SLC25A46):c.10+431T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00453 in 227,794 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0067 ( 16 hom., cov: 32)
Exomes 𝑓: 0.00017 ( 0 hom. )
Consequence
SLC25A46
NM_001303250.3 intron
NM_001303250.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.859
Genes affected
SLC25A46 (HGNC:25198): (solute carrier family 25 member 46) This gene encodes a mitochondrial solute carrier protein family member. It functions in promoting mitochondrial fission, and prevents the formation of hyperfilamentous mitochondria. Mutation of this gene results in neuropathy and optic atrophy. [provided by RefSeq, Aug 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 5-110738678-T-C is Benign according to our data. Variant chr5-110738678-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1187279.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00669 (1018/152172) while in subpopulation AFR AF= 0.0238 (989/41528). AF 95% confidence interval is 0.0226. There are 16 homozygotes in gnomad4. There are 465 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 16 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A46 | NM_001303250.3 | c.10+431T>C | intron_variant | ||||
TMEM232 | XM_006714670.4 | c.-298+44A>G | intron_variant | ||||
TMEM232 | XM_011543552.3 | c.-649+44A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A46 | ENST00000513807.5 | c.-204+431T>C | intron_variant | 2 | |||||
TMEM232 | ENST00000515278.6 | c.-298+44A>G | intron_variant | 5 | |||||
TMEM232 | ENST00000503527.6 | n.197+44A>G | intron_variant, non_coding_transcript_variant | 3 | |||||
SLC25A46 | ENST00000508781.5 | n.112+431T>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00667 AC: 1014AN: 152054Hom.: 16 Cov.: 32
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GnomAD4 exome AF: 0.000172 AC: 13AN: 75622Hom.: 0 Cov.: 0 AF XY: 0.000150 AC XY: 6AN XY: 40106
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GnomAD4 genome ? AF: 0.00669 AC: 1018AN: 152172Hom.: 16 Cov.: 32 AF XY: 0.00625 AC XY: 465AN XY: 74398
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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 | Jul 15, 2018 | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at