13-24222973-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001166271.3(SPATA13):c.44A>G(p.Asn15Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000284 in 1,551,178 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict 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. N15I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001166271.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA13 | NM_001166271.3 | c.44A>G | p.Asn15Ser | missense_variant | 2/13 | ENST00000382108.8 | |
SPATA13 | NM_001286792.2 | c.230A>G | p.Asn77Ser | missense_variant | 4/15 | ||
SPATA13 | NM_153023.4 | c.-222-26504A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA13 | ENST00000382108.8 | c.44A>G | p.Asn15Ser | missense_variant | 2/13 | 5 | NM_001166271.3 | ||
SPATA13 | ENST00000424834.6 | c.44A>G | p.Asn15Ser | missense_variant | 4/15 | 1 | |||
SPATA13 | ENST00000382095.8 | c.-222-26504A>G | intron_variant | 2 | |||||
SPATA13 | ENST00000466831.2 | n.366A>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000260 AC: 4AN: 154024Hom.: 0 AF XY: 0.0000367 AC XY: 3AN XY: 81778
GnomAD4 exome AF: 0.0000264 AC: 37AN: 1398982Hom.: 0 Cov.: 29 AF XY: 0.0000217 AC XY: 15AN XY: 689960
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.44A>G (p.N15S) alteration is located in exon 2 (coding exon 1) of the SPATA13 gene. This alteration results from a A to G substitution at nucleotide position 44, causing the asparagine (N) at amino acid position 15 to be replaced by a serine (S). 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