rs780650245
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 4P and 5B. PVS1_ModeratePM2BP6BS1
The NM_003705.5(SLC25A12):c.2015delC(p.Ala672GlufsTer20) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,614,200 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003705.5 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A12 | NM_003705.5 | c.2015delC | p.Ala672GlufsTer20 | frameshift_variant | Exon 18 of 18 | ENST00000422440.7 | NP_003696.2 | |
SLC25A12 | XM_047446142.1 | c.1742delC | p.Ala581GlufsTer20 | frameshift_variant | Exon 16 of 16 | XP_047302098.1 | ||
SLC25A12 | NR_047549.2 | n.1929delC | non_coding_transcript_exon_variant | Exon 17 of 17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A12 | ENST00000422440.7 | c.2015delC | p.Ala672GlufsTer20 | frameshift_variant | Exon 18 of 18 | 1 | NM_003705.5 | ENSP00000388658.2 | ||
SLC25A12 | ENST00000263812.8 | n.*1635delC | non_coding_transcript_exon_variant | Exon 17 of 17 | 2 | ENSP00000263812.4 | ||||
SLC25A12 | ENST00000472070.1 | n.1425delC | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 | |||||
SLC25A12 | ENST00000263812.8 | n.*1635delC | 3_prime_UTR_variant | Exon 17 of 17 | 2 | ENSP00000263812.4 |
Frequencies
GnomAD3 genomes AF: 0.000539 AC: 82AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000151 AC: 38AN: 251454Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135898
GnomAD4 exome AF: 0.0000670 AC: 98AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.0000591 AC XY: 43AN XY: 727238
GnomAD4 genome AF: 0.000538 AC: 82AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.000483 AC XY: 36AN XY: 74502
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 39 Uncertain:1
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at