chr16-12048618-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032167.5(SNX29):c.746C>T(p.Ala249Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,670 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032167.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNX29 | NM_032167.5 | c.746C>T | p.Ala249Val | missense_variant, splice_region_variant | 7/21 | ENST00000566228.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNX29 | ENST00000566228.6 | c.746C>T | p.Ala249Val | missense_variant, splice_region_variant | 7/21 | 5 | NM_032167.5 | P1 | |
SNX29 | ENST00000564111.5 | n.808C>T | splice_region_variant, non_coding_transcript_exon_variant | 7/8 | 2 | ||||
SNX29 | ENST00000568359.1 | n.577C>T | splice_region_variant, non_coding_transcript_exon_variant | 4/5 | 5 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461670Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727144
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 03, 2022 | The c.746C>T (p.A249V) alteration is located in exon 1 (coding exon 1) of the SNX29 gene. This alteration results from a C to T substitution at nucleotide position 746, causing the alanine (A) at amino acid position 249 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