chr13-24223312-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001166271.3(SPATA13):c.383G>A(p.Arg128Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000111 in 1,551,522 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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.383G>A | p.Arg128Gln | missense_variant | 2/13 | ENST00000382108.8 | |
SPATA13 | NM_001286792.2 | c.569G>A | p.Arg190Gln | missense_variant | 4/15 | ||
SPATA13 | NM_153023.4 | c.-222-26165G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA13 | ENST00000382108.8 | c.383G>A | p.Arg128Gln | missense_variant | 2/13 | 5 | NM_001166271.3 | ||
SPATA13 | ENST00000424834.6 | c.383G>A | p.Arg128Gln | missense_variant | 4/15 | 1 | |||
SPATA13 | ENST00000382095.8 | c.-222-26165G>A | intron_variant | 2 | |||||
SPATA13 | ENST00000466831.2 | n.705G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000224 AC: 35AN: 156120Hom.: 0 AF XY: 0.000338 AC XY: 28AN XY: 82778
GnomAD4 exome AF: 0.000115 AC: 161AN: 1399196Hom.: 0 Cov.: 29 AF XY: 0.000180 AC XY: 124AN XY: 690118
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.383G>A (p.R128Q) alteration is located in exon 2 (coding exon 1) of the SPATA13 gene. This alteration results from a G to A substitution at nucleotide position 383, causing the arginine (R) at amino acid position 128 to be replaced by a glutamine (Q). 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