chr15-45402676-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024063.3(SPATA5L1):c.247G>A(p.Ala83Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000702 in 1,424,210 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024063.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA5L1 | NM_024063.3 | c.247G>A | p.Ala83Thr | missense_variant | 1/8 | ENST00000305560.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AFG2B | ENST00000305560.11 | c.247G>A | p.Ala83Thr | missense_variant | 1/8 | 1 | NM_024063.3 | P1 | |
AFG2B | ENST00000559860.2 | n.307G>A | non_coding_transcript_exon_variant | 1/5 | 2 | ||||
AFG2B | ENST00000531970.5 | c.247G>A | p.Ala83Thr | missense_variant, NMD_transcript_variant | 1/8 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000552 AC: 1AN: 181308Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 100752
GnomAD4 exome AF: 7.02e-7 AC: 1AN: 1424210Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 706566
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 07, 2021 | The c.247G>A (p.A83T) alteration is located in exon 1 (coding exon 1) of the SPATA5L1 gene. This alteration results from a G to A substitution at nucleotide position 247, causing the alanine (A) at amino acid position 83 to be replaced by a threonine (T). 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