9-34723287-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001141917.2(SPATA31F1):c.3953G>A(p.Cys1318Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,399,424 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001141917.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPATA31F1 | NM_001141917.2 | c.3953G>A | p.Cys1318Tyr | missense_variant | Exon 4 of 4 | ENST00000378788.4 | NP_001135389.1 | |
PHF24 | XM_047423102.1 | c.133+20249C>T | intron_variant | Intron 4 of 11 | XP_047279058.1 | |||
PHF24 | XM_047423103.1 | c.70+20249C>T | intron_variant | Intron 2 of 9 | XP_047279059.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1399424Hom.: 0 Cov.: 66 AF XY: 0.00 AC XY: 0AN XY: 690220
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3953G>A (p.C1318Y) alteration is located in exon 4 (coding exon 4) of the FAM205A gene. This alteration results from a G to A substitution at nucleotide position 3953, causing the cysteine (C) at amino acid position 1318 to be replaced by a tyrosine (Y). 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
Publications
No publications associated with this variant yet.