chr9-81947336-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_207416.3(SPATA31D3):c.2083C>T(p.Arg695Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_207416.3 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 |
---|---|---|---|---|---|---|---|---|
SPATA31D3 | NM_207416.3 | c.2083C>T | p.Arg695Cys | missense_variant | Exon 4 of 4 | ENST00000445385.3 | NP_997299.2 | |
LOC105376105 | NR_188610.1 | n.943-850G>A | intron_variant | Intron 3 of 5 | ||||
LOC105376105 | NR_188611.1 | n.943-850G>A | intron_variant | Intron 3 of 5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPATA31D3 | ENST00000445385.3 | c.2083C>T | p.Arg695Cys | missense_variant | Exon 4 of 4 | 1 | NM_207416.3 | ENSP00000488117.1 | ||
ENSG00000267559 | ENST00000585776.5 | n.943-850G>A | intron_variant | Intron 3 of 4 | 2 | |||||
ENSG00000267559 | ENST00000592744.1 | n.519-850G>A | intron_variant | Intron 3 of 3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 47898Hom.: 0 Cov.: 6 FAILED QC
GnomAD3 exomes AF: 0.0000549 AC: 3AN: 54642Hom.: 0 AF XY: 0.0000724 AC XY: 2AN XY: 27634
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000477 AC: 28AN: 587452Hom.: 0 Cov.: 8 AF XY: 0.0000561 AC XY: 17AN XY: 303062
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000209 AC: 1AN: 47898Hom.: 0 Cov.: 6 AF XY: 0.0000458 AC XY: 1AN XY: 21848
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2083C>T (p.R695C) alteration is located in exon 4 (coding exon 4) of the SPATA31D3 gene. This alteration results from a C to T substitution at nucleotide position 2083, causing the arginine (R) at amino acid position 695 to be replaced by a cysteine (C). 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