9-112864254-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001012994.2(SNX30):c.1109C>T(p.Ala370Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,613,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001012994.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNX30 | NM_001012994.2 | c.1109C>T | p.Ala370Val | missense_variant | 8/9 | ENST00000374232.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNX30 | ENST00000374232.8 | c.1109C>T | p.Ala370Val | missense_variant | 8/9 | 5 | NM_001012994.2 | P1 | |
SNX30 | ENST00000416585.1 | c.209C>T | p.Ala70Val | missense_variant | 3/4 | 3 | |||
SNX30 | ENST00000604751.1 | n.104C>T | non_coding_transcript_exon_variant | 2/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249422Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135338
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461584Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727088
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.1109C>T (p.A370V) alteration is located in exon 8 (coding exon 8) of the SNX30 gene. This alteration results from a C to T substitution at nucleotide position 1109, causing the alanine (A) at amino acid position 370 to be replaced by a valine (V). 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