chr1-43150797-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001101376.3(CFAP144):āc.170A>Gā(p.Asp57Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,610,570 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001101376.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP144 | NM_001101376.3 | c.170A>G | p.Asp57Gly | missense_variant | 2/4 | ENST00000335282.5 | |
CFAP144 | XM_005270875.6 | c.170A>G | p.Asp57Gly | missense_variant | 2/4 | ||
CFAP144 | XM_005270876.5 | c.86A>G | p.Asp29Gly | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP144 | ENST00000335282.5 | c.170A>G | p.Asp57Gly | missense_variant | 2/4 | 2 | NM_001101376.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000111 AC: 27AN: 243286Hom.: 0 AF XY: 0.0000986 AC XY: 13AN XY: 131834
GnomAD4 exome AF: 0.0000261 AC: 38AN: 1458386Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 725094
GnomAD4 genome AF: 0.000105 AC: 16AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2024 | The c.170A>G (p.D57G) alteration is located in exon 2 (coding exon 2) of the FAM183A gene. This alteration results from a A to G substitution at nucleotide position 170, causing the aspartic acid (D) at amino acid position 57 to be replaced by a glycine (G). 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