10-124681738-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_014661.4(FAM53B):c.775C>T(p.Arg259Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,610,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014661.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM53B | ENST00000337318.8 | c.775C>T | p.Arg259Cys | missense_variant | Exon 4 of 5 | 1 | NM_014661.4 | ENSP00000338532.3 | ||
ENSG00000258539 | ENST00000494792.1 | n.*972C>T | non_coding_transcript_exon_variant | Exon 9 of 10 | 5 | ENSP00000455755.1 | ||||
ENSG00000258539 | ENST00000494792.1 | n.*972C>T | 3_prime_UTR_variant | Exon 9 of 10 | 5 | ENSP00000455755.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152266Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000167 AC: 4AN: 239954Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 130418
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1457866Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 724886
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74396
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.775C>T (p.R259C) alteration is located in exon 4 (coding exon 3) of the FAM53B gene. This alteration results from a C to T substitution at nucleotide position 775, causing the arginine (R) at amino acid position 259 to be replaced by a cysteine (C). 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