NM_001145196.1:c.117C>A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001145196.1(SPATA31A6):c.117C>A(p.Phe39Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000521 in 1,534,714 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145196.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000147 AC: 2AN: 136080Hom.: 0 Cov.: 23
GnomAD4 exome AF: 0.00000429 AC: 6AN: 1398634Hom.: 2 Cov.: 34 AF XY: 0.00000718 AC XY: 5AN XY: 696032
GnomAD4 genome AF: 0.0000147 AC: 2AN: 136080Hom.: 0 Cov.: 23 AF XY: 0.0000302 AC XY: 2AN XY: 66238
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.117C>A (p.F39L) alteration is located in exon 1 (coding exon 1) of the SPATA31A6 gene. This alteration results from a C to A substitution at nucleotide position 117, causing the phenylalanine (F) at amino acid position 39 to be replaced by a leucine (L). 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