rs2236711
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014758.3(SNX19):c.*9033C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 152,064 control chromosomes in the GnomAD database, including 14,825 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.44 ( 14825 hom., cov: 34)
Exomes 𝑓: 0.50 ( 0 hom. )
Consequence
SNX19
NM_014758.3 3_prime_UTR
NM_014758.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.981
Genes affected
SNX19 (HGNC:21532): (sorting nexin 19) Islet antigen-2 (IA-2) is an autoantigen in type 1 diabetes and plays a role in insulin secretion. IA-2 is found in dense-core secretory vesicles and interacts with the product of this gene, a sorting nexin. In mouse pancreatic beta-cells, the encoded protein influenced insulin secretion by stabilizing the number of dense-core secretory vesicles. [provided by RefSeq, Dec 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNX19 | NM_014758.3 | c.*9033C>T | 3_prime_UTR_variant | 11/11 | ENST00000265909.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNX19 | ENST00000265909.9 | c.*9033C>T | 3_prime_UTR_variant | 11/11 | 1 | NM_014758.3 | P1 | ||
ENST00000525716.2 | n.859C>T | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.438 AC: 66485AN: 151944Hom.: 14827 Cov.: 34
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GnomAD4 exome AF: 0.500 AC: 1AN: 2Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1AN XY: 2
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GnomAD4 genome ? AF: 0.437 AC: 66504AN: 152062Hom.: 14825 Cov.: 34 AF XY: 0.440 AC XY: 32695AN XY: 74336
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at