4-185143468-C-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001151.4(SLC25A4):c.96C>G(p.Val32=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000134 in 1,487,706 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 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 7.5e-7 ( 0 hom. )
Consequence
SLC25A4
NM_001151.4 synonymous
NM_001151.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0510
Genes affected
SLC25A4 (HGNC:10990): (solute carrier family 25 member 4) This gene is a member of the mitochondrial carrier subfamily of solute carrier protein genes. The product of this gene functions as a gated pore that translocates ADP from the cytoplasm into the mitochondrial matrix and ATP from the mitochondrial matrix into the cytoplasm. The protein forms a homodimer embedded in the inner mitochondria membrane. Mutations in this gene have been shown to result in autosomal dominant progressive external opthalmoplegia and familial hypertrophic cardiomyopathy. [provided by RefSeq, Jun 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
BP6
?
Variant 4-185143468-C-G is Benign according to our data. Variant chr4-185143468-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2102571.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.051 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A4 | NM_001151.4 | c.96C>G | p.Val32= | synonymous_variant | 1/4 | ENST00000281456.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A4 | ENST00000281456.11 | c.96C>G | p.Val32= | synonymous_variant | 1/4 | 1 | NM_001151.4 | P1 | |
SLC25A4 | ENST00000491736.1 | c.96C>G | p.Val32= | synonymous_variant, NMD_transcript_variant | 1/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000661 AC: 1AN: 151298Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00000854 AC: 1AN: 117152Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 63170
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GnomAD4 exome AF: 7.48e-7 AC: 1AN: 1336408Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 659180
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GnomAD4 genome ? AF: 0.00000661 AC: 1AN: 151298Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 73916
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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 | Feb 23, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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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