10-58386214-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_003201.3(TFAM):c.102-6A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000352 in 1,421,104 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_003201.3 splice_region, splice_polypyrimidine_tract, 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 |
---|---|---|---|---|---|---|---|
TFAM | NM_003201.3 | c.102-6A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000487519.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TFAM | ENST00000487519.6 | c.102-6A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003201.3 | P1 | |||
TFAM | ENST00000373895.7 | c.102-6A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
TFAM | ENST00000395377.2 | c.46-6A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
TFAM | ENST00000373899.3 | n.305-6A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000352 AC: 5AN: 1421104Hom.: 0 Cov.: 27 AF XY: 0.00000564 AC XY: 4AN XY: 709668
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
TFAM-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 16, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.