rs2067000
Positions:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_StrongBS1
The NM_001349335.2(SLC25A48):c.-521+36909A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.025 in 126,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.025 ( 0 hom., cov: 21)
Failed GnomAD Quality Control
Consequence
SLC25A48
NM_001349335.2 intron
NM_001349335.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.878
Genes affected
SLC25A48 (HGNC:30451): (solute carrier family 25 member 48) Predicted to enable acyl carnitine transmembrane transporter activity. Predicted to be involved in acyl carnitine transport and amino acid transport. Predicted to be located in mitochondrial inner membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.025 (3174/126826) while in subpopulation NFE AF= 0.0273 (1619/59254). AF 95% confidence interval is 0.0262. There are 0 homozygotes in gnomad4. There are 1484 alleles in male gnomad4 subpopulation. Median coverage is 21. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A48 | NM_001349335.2 | c.-521+36909A>C | intron_variant | ||||
SLC25A48 | NM_001349345.2 | c.-521+36909A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A48 | ENST00000646290.1 | c.-521+36909A>C | intron_variant | ||||||
SLC25A48 | ENST00000647391.1 | n.829+118A>C | intron_variant, non_coding_transcript_variant | ||||||
SLC25A48 | ENST00000698885.1 | n.365-89159A>C | intron_variant, non_coding_transcript_variant | ||||||
SLC25A48 | ENST00000698886.1 | n.751+36909A>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0250 AC: 3171AN: 126746Hom.: 0 Cov.: 21
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21
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0250 AC: 3174AN: 126826Hom.: 0 Cov.: 21 AF XY: 0.0242 AC XY: 1484AN XY: 61328
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at