1-108139059-TTGAGCCTGCA-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_013386.5(SLC25A24):βc.1238_1247delβ(p.Met413LysfsTer4) variant causes a frameshift, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000253 in 1,583,464 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (β ).
Frequency
Genomes: π 0.000020 ( 0 hom., cov: 32)
Exomes π: 7.0e-7 ( 0 hom. )
Consequence
SLC25A24
NM_013386.5 frameshift, splice_region
NM_013386.5 frameshift, splice_region
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.91
Genes affected
SLC25A24 (HGNC:20662): (solute carrier family 25 member 24) This gene encodes a carrier protein that transports ATP-Mg exchanging it for phosphate. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 1-108139059-TTGAGCCTGCA-T is Benign according to our data. Variant chr1-108139059-TTGAGCCTGCA-T is described in ClinVar as [Likely_benign]. Clinvar id is 2781678.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A24 | NM_013386.5 | c.1238_1247del | p.Met413LysfsTer4 | frameshift_variant, splice_region_variant | 9/10 | ENST00000565488.6 | |
SLC25A24 | NM_213651.3 | c.1181_1190del | p.Met394LysfsTer4 | frameshift_variant, splice_region_variant | 9/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A24 | ENST00000565488.6 | c.1238_1247del | p.Met413LysfsTer4 | frameshift_variant, splice_region_variant | 9/10 | 1 | NM_013386.5 | P1 | |
SLC25A24 | ENST00000370041.4 | c.1181_1190del | p.Met394LysfsTer4 | frameshift_variant, splice_region_variant | 9/10 | 1 | |||
SLC25A24 | ENST00000264128.13 | c.*817_*826del | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 8/9 | 5 | ||||
SLC25A24 | ENST00000648874.1 | c.*559_*568del | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 10/11 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152176Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
3
AN:
152176
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00000435 AC: 1AN: 229840Hom.: 0 AF XY: 0.00000804 AC XY: 1AN XY: 124302
GnomAD3 exomes
AF:
AC:
1
AN:
229840
Hom.:
AF XY:
AC XY:
1
AN XY:
124302
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 6.99e-7 AC: 1AN: 1431288Hom.: 0 AF XY: 0.00000141 AC XY: 1AN XY: 709784
GnomAD4 exome
AF:
AC:
1
AN:
1431288
Hom.:
AF XY:
AC XY:
1
AN XY:
709784
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
GnomAD4 genome
AF:
AC:
3
AN:
152176
Hom.:
Cov.:
32
AF XY:
AC XY:
2
AN XY:
74346
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
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 | Jan 15, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at