22-48646671-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The ENST00000402357.6(TAFA5):c.187C>T(p.Arg63Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000176 in 1,611,616 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R63Q) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000402357.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TAFA5 | NM_001082967.3 | c.187C>T | p.Arg63Trp | missense_variant | 2/4 | ENST00000402357.6 | NP_001076436.1 | |
TAFA5 | NM_015381.7 | c.166C>T | p.Arg56Trp | missense_variant | 2/4 | NP_056196.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TAFA5 | ENST00000402357.6 | c.187C>T | p.Arg63Trp | missense_variant | 2/4 | 1 | NM_001082967.3 | ENSP00000383933 | P4 | |
TAFA5 | ENST00000336769.9 | c.187C>T | p.Arg63Trp | missense_variant | 2/4 | 4 | ENSP00000336812 | |||
TAFA5 | ENST00000358295.9 | c.166C>T | p.Arg56Trp | missense_variant | 2/4 | 2 | ENSP00000351043 | A1 | ||
TAFA5 | ENST00000473898.1 | n.120-61046C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000249 AC: 61AN: 244756Hom.: 0 AF XY: 0.000262 AC XY: 35AN XY: 133702
GnomAD4 exome AF: 0.000182 AC: 265AN: 1459428Hom.: 0 Cov.: 31 AF XY: 0.000190 AC XY: 138AN XY: 726106
GnomAD4 genome AF: 0.000118 AC: 18AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 25, 2022 | The c.187C>T (p.R63W) alteration is located in exon 2 (coding exon 2) of the FAM19A5 gene. This alteration results from a C to T substitution at nucleotide position 187, causing the arginine (R) at amino acid position 63 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