1-48453026-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_019073.4(SPATA6):c.157C>G(p.Leu53Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000258 in 1,613,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019073.4 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 | UniProt |
---|---|---|---|---|---|---|---|
SPATA6 | NM_019073.4 | c.157C>G | p.Leu53Val | missense_variant | 2/13 | ENST00000371847.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA6 | ENST00000371847.8 | c.157C>G | p.Leu53Val | missense_variant | 2/13 | 1 | NM_019073.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000132 AC: 33AN: 250944Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135626
GnomAD4 exome AF: 0.000271 AC: 396AN: 1461476Hom.: 0 Cov.: 30 AF XY: 0.000264 AC XY: 192AN XY: 727046
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2023 | The c.157C>G (p.L53V) alteration is located in exon 2 (coding exon 2) of the SPATA6 gene. This alteration results from a C to G substitution at nucleotide position 157, causing the leucine (L) at amino acid position 53 to be replaced by a valine (V). 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