chr6-30577854-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_001025091.2(ABCF1):c.157G>A(p.Gly53Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,613,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001025091.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCF1 | NM_001025091.2 | c.157G>A | p.Gly53Arg | missense_variant | 3/25 | ENST00000326195.13 | |
ABCF1 | NM_001090.3 | c.157G>A | p.Gly53Arg | missense_variant | 3/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCF1 | ENST00000326195.13 | c.157G>A | p.Gly53Arg | missense_variant | 3/25 | 1 | NM_001025091.2 | A1 | |
ABCF1 | ENST00000376545.7 | c.157G>A | p.Gly53Arg | missense_variant | 3/24 | 1 | |||
ABCF1 | ENST00000441867.6 | c.157G>A | p.Gly53Arg | missense_variant | 3/25 | 5 | P3 | ||
ABCF1 | ENST00000468958.1 | c.-135G>A | 5_prime_UTR_variant | 2/7 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152134Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 245584Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133738
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461698Hom.: 0 Cov.: 34 AF XY: 0.0000220 AC XY: 16AN XY: 727142
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152134Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 24, 2023 | The c.157G>A (p.G53R) alteration is located in exon 3 (coding exon 3) of the ABCF1 gene. This alteration results from a G to A substitution at nucleotide position 157, causing the glycine (G) at amino acid position 53 to be replaced by an arginine (R). 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