9-61192079-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_015667.2(SPATA31A7):c.248C>G(p.Ala83Gly) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 6/9 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015667.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPATA31A7 | NM_015667.2 | c.248C>G | p.Ala83Gly | missense_variant, splice_region_variant | Exon 3 of 4 | ENST00000619167.2 | NP_056482.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000779 AC: 1AN: 128426Hom.: 0 Cov.: 19
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000142 AC: 2AN: 1407552Hom.: 0 Cov.: 32 AF XY: 0.00000143 AC XY: 1AN XY: 699974
GnomAD4 genome AF: 0.00000779 AC: 1AN: 128426Hom.: 0 Cov.: 19 AF XY: 0.0000160 AC XY: 1AN XY: 62314
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.248C>G (p.A83G) alteration is located in exon 3 (coding exon 3) of the SPATA31A7 gene. This alteration results from a C to G substitution at nucleotide position 248, causing the alanine (A) at amino acid position 83 to be replaced by a glycine (G). 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