5-148335627-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001040433.2(SPINK9):c.14C>G(p.Ala5Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,613,648 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001040433.2 missense
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 |
---|---|---|---|---|---|---|---|---|
SPINK9 | NM_001040433.2 | c.14C>G | p.Ala5Gly | missense_variant | Exon 1 of 4 | ENST00000377906.2 | NP_001035523.1 | |
SPINK9 | XM_017009709.2 | c.119-795C>G | intron_variant | Intron 1 of 3 | XP_016865198.1 | |||
FBXO38-DT | NR_105057.1 | n.497-27462G>C | intron_variant | Intron 2 of 4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 251144Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135756
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461340Hom.: 1 Cov.: 30 AF XY: 0.0000316 AC XY: 23AN XY: 727000
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.14C>G (p.A5G) alteration is located in exon 1 (coding exon 1) of the SPINK9 gene. This alteration results from a C to G substitution at nucleotide position 14, causing the alanine (A) at amino acid position 5 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