chr1-109924063-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000757.6(CSF1):c.1442A>T(p.His481Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000757.6 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSF1 | NM_000757.6 | c.1442A>T | p.His481Leu | missense_variant | 6/9 | ENST00000329608.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF1 | ENST00000329608.11 | c.1442A>T | p.His481Leu | missense_variant | 6/9 | 1 | NM_000757.6 | P4 | |
CSF1 | ENST00000369802.7 | c.1442A>T | p.His481Leu | missense_variant | 6/9 | 1 | P4 | ||
CSF1 | ENST00000369801.1 | c.1094A>T | p.His365Leu | missense_variant | 7/9 | 1 | |||
CSF1 | ENST00000420111.6 | c.548A>T | p.His183Leu | missense_variant | 6/9 | 5 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251372Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135906
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461874Hom.: 0 Cov.: 83 AF XY: 0.00 AC XY: 0AN XY: 727242
GnomAD4 genome ? Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.1442A>T (p.H481L) alteration is located in exon 1 (coding exon 1) of the CSF1 gene. This alteration results from a A to T substitution at nucleotide position 1442, causing the histidine (H) at amino acid position 481 to be replaced by a leucine (L). 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