13-107170696-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080396.3(NALF1):āc.1178T>Cā(p.Val393Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000173 in 1,614,172 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001080396.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NALF1 | NM_001080396.3 | c.1178T>C | p.Val393Ala | missense_variant | 3/3 | ENST00000375915.4 | NP_001073865.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NALF1 | ENST00000375915.4 | c.1178T>C | p.Val393Ala | missense_variant | 3/3 | 1 | NM_001080396.3 | ENSP00000365080.1 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000159 AC: 40AN: 251472Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135910
GnomAD4 exome AF: 0.000175 AC: 256AN: 1461882Hom.: 1 Cov.: 31 AF XY: 0.000184 AC XY: 134AN XY: 727240
GnomAD4 genome AF: 0.000151 AC: 23AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 29, 2023 | The c.1178T>C (p.V393A) alteration is located in exon 3 (coding exon 3) of the FAM155A gene. This alteration results from a T to C substitution at nucleotide position 1178, causing the valine (V) at amino acid position 393 to be replaced by an alanine (A). 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