9-42183860-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001145196.1(SPATA31A6):c.173C>T(p.Ser58Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000015 in 1,531,920 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000220 AC: 3AN: 136266Hom.: 0 Cov.: 24
GnomAD4 exome AF: 0.0000143 AC: 20AN: 1395654Hom.: 3 Cov.: 34 AF XY: 0.0000158 AC XY: 11AN XY: 694556
GnomAD4 genome AF: 0.0000220 AC: 3AN: 136266Hom.: 0 Cov.: 24 AF XY: 0.0000452 AC XY: 3AN XY: 66348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.173C>T (p.S58L) alteration is located in exon 1 (coding exon 1) of the SPATA31A6 gene. This alteration results from a C to T substitution at nucleotide position 173, causing the serine (S) at amino acid position 58 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