chr13-24222973-A-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001166271.3(SPATA13):c.44A>T(p.Asn15Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000406 in 1,551,296 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. N15S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001166271.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA13 | NM_001166271.3 | c.44A>T | p.Asn15Ile | missense_variant | 2/13 | ENST00000382108.8 | |
SPATA13 | NM_001286792.2 | c.230A>T | p.Asn77Ile | missense_variant | 4/15 | ||
SPATA13 | NM_153023.4 | c.-222-26504A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA13 | ENST00000382108.8 | c.44A>T | p.Asn15Ile | missense_variant | 2/13 | 5 | NM_001166271.3 | ||
SPATA13 | ENST00000424834.6 | c.44A>T | p.Asn15Ile | missense_variant | 4/15 | 1 | |||
SPATA13 | ENST00000382095.8 | c.-222-26504A>T | intron_variant | 2 | |||||
SPATA13 | ENST00000466831.2 | n.366A>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000223 AC: 34AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000714 AC: 11AN: 154024Hom.: 0 AF XY: 0.0000734 AC XY: 6AN XY: 81778
GnomAD4 exome AF: 0.0000200 AC: 28AN: 1398982Hom.: 0 Cov.: 29 AF XY: 0.0000232 AC XY: 16AN XY: 689960
GnomAD4 genome AF: 0.000230 AC: 35AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2023 | The c.44A>T (p.N15I) alteration is located in exon 2 (coding exon 1) of the SPATA13 gene. This alteration results from a A to T substitution at nucleotide position 44, causing the asparagine (N) at amino acid position 15 to be replaced by an isoleucine (I). 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