6-30577454-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001025091.2(ABCF1):c.119C>T(p.Thr40Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,226 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict 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 Uncertain significance (★).
Frequency
Consequence
NM_001025091.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCF1 | NM_001025091.2 | c.119C>T | p.Thr40Met | missense_variant, splice_region_variant | Exon 2 of 25 | ENST00000326195.13 | NP_001020262.1 | |
ABCF1 | NM_001090.3 | c.119C>T | p.Thr40Met | missense_variant, splice_region_variant | Exon 2 of 24 | NP_001081.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCF1 | ENST00000326195.13 | c.119C>T | p.Thr40Met | missense_variant, splice_region_variant | Exon 2 of 25 | 1 | NM_001025091.2 | ENSP00000313603.8 | ||
ABCF1 | ENST00000376545.7 | c.119C>T | p.Thr40Met | missense_variant, splice_region_variant | Exon 2 of 24 | 1 | ENSP00000365728.3 | |||
ABCF1 | ENST00000441867.6 | c.119C>T | p.Thr40Met | missense_variant, splice_region_variant | Exon 2 of 25 | 5 | ENSP00000405512.2 | |||
ABCF1 | ENST00000468958.1 | c.-171-364C>T | intron_variant | Intron 1 of 6 | 3 | ENSP00000440893.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152018Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250478Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135408
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461208Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726896
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152018Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74250
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.119C>T (p.T40M) alteration is located in exon 2 (coding exon 2) of the ABCF1 gene. This alteration results from a C to T substitution at nucleotide position 119, causing the threonine (T) at amino acid position 40 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at