1-166070399-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001017961.5(FAM78B):c.628C>T(p.Arg210Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,614,110 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001017961.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM78B | NM_001017961.5 | c.628C>T | p.Arg210Trp | missense_variant | Exon 2 of 2 | ENST00000354422.4 | NP_001017961.1 | |
FAM78B | NM_001320302.2 | c.264-9736C>T | intron_variant | Intron 1 of 1 | NP_001307231.1 | |||
FAM78B | NR_135199.2 | n.1381C>T | non_coding_transcript_exon_variant | Exon 2 of 3 | ||||
FAM78B | NR_163271.1 | n.1135C>T | non_coding_transcript_exon_variant | Exon 2 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251176Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135740
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461820Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727208
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.628C>T (p.R210W) alteration is located in exon 2 (coding exon 2) of the FAM78B gene. This alteration results from a C to T substitution at nucleotide position 628, causing the arginine (R) at amino acid position 210 to be replaced by a tryptophan (W). 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