9-34723309-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001141917.2(SPATA31F1):c.3931G>A(p.Ala1311Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000214 in 1,399,394 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A1311P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001141917.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPATA31F1 | NM_001141917.2 | c.3931G>A | p.Ala1311Thr | missense_variant | Exon 4 of 4 | ENST00000378788.4 | NP_001135389.1 | |
PHF24 | XM_047423102.1 | c.133+20271C>T | intron_variant | Intron 4 of 11 | XP_047279058.1 | |||
PHF24 | XM_047423103.1 | c.70+20271C>T | intron_variant | Intron 2 of 9 | XP_047279059.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000214 AC: 3AN: 1399394Hom.: 0 Cov.: 67 AF XY: 0.00000145 AC XY: 1AN XY: 690202
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.