11-133842554-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_174927.3(SPATA19):c.368G>A(p.Arg123His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,580 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_174927.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPATA19 | NM_174927.3 | c.368G>A | p.Arg123His | missense_variant | Exon 5 of 7 | ENST00000299140.8 | NP_777587.1 | |
SPATA19 | NM_001291992.2 | c.368G>A | p.Arg123His | missense_variant | Exon 5 of 7 | NP_001278921.1 | ||
SPATA19 | XR_947806.2 | n.435G>A | non_coding_transcript_exon_variant | Exon 5 of 8 | ||||
SPATA19 | XR_947807.2 | n.435G>A | non_coding_transcript_exon_variant | Exon 5 of 8 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251484Hom.: 1 AF XY: 0.0000589 AC XY: 8AN XY: 135914
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461500Hom.: 1 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 727086
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.368G>A (p.R123H) alteration is located in exon 5 (coding exon 5) of the SPATA19 gene. This alteration results from a G to A substitution at nucleotide position 368, causing the arginine (R) at amino acid position 123 to be replaced by a histidine (H). 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