9-61191465-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_015667.2(SPATA31A7):c.202C>T(p.Arg68Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 1,272,846 control chromosomes in the GnomAD database, including 46 homozygotes. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R68Q) has been classified 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPATA31A7 | NM_015667.2 | c.202C>T | p.Arg68Trp | missense_variant | Exon 2 of 4 | ENST00000619167.2 | NP_056482.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 21AN: 116286Hom.: 6 Cov.: 17 FAILED QC
GnomAD3 exomes AF: 0.0000553 AC: 13AN: 235194Hom.: 3 AF XY: 0.0000391 AC XY: 5AN XY: 127848
GnomAD4 exome AF: 0.000130 AC: 166AN: 1272846Hom.: 46 Cov.: 30 AF XY: 0.000160 AC XY: 101AN XY: 631634
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000181 AC: 21AN: 116286Hom.: 6 Cov.: 17 AF XY: 0.000160 AC XY: 9AN XY: 56234
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.202C>T (p.R68W) alteration is located in exon 2 (coding exon 2) of the SPATA31A7 gene. This alteration results from a C to T substitution at nucleotide position 202, causing the arginine (R) at amino acid position 68 to be replaced by a tryptophan (W). 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