19-5679338-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_205767.3(MICOS13):c.259+7C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,612,374 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_205767.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MICOS13 | NM_205767.3 | c.259+7C>A | splice_region_variant, intron_variant | ENST00000309324.9 | |||
MICOS13 | NM_001308240.2 | c.325+7C>A | splice_region_variant, intron_variant | ||||
MICOS13 | NM_001365761.2 | c.325+7C>A | splice_region_variant, intron_variant | ||||
MICOS13 | XM_011527675.3 | c.325+7C>A | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICOS13 | ENST00000309324.9 | c.259+7C>A | splice_region_variant, intron_variant | 1 | NM_205767.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248804Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134902
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460188Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726402
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74356
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 24, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at