9-61192779-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_015667.2(SPATA31A7):c.693C>A(p.Asp231Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 7/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015667.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPATA31A7 | NM_015667.2 | c.693C>A | p.Asp231Glu | missense_variant | Exon 4 of 4 | ENST00000619167.2 | NP_056482.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 143AN: 27222Hom.: 4 Cov.: 5 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00773 AC: 4785AN: 618772Hom.: 399 Cov.: 8 AF XY: 0.00747 AC XY: 2376AN XY: 318196
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00525 AC: 143AN: 27244Hom.: 4 Cov.: 5 AF XY: 0.00489 AC XY: 60AN XY: 12272
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.693C>A (p.D231E) alteration is located in exon 4 (coding exon 4) of the SPATA31A7 gene. This alteration results from a C to A substitution at nucleotide position 693, causing the aspartic acid (D) at amino acid position 231 to be replaced by a glutamic acid (E). 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