17-353140-C-CA
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The ENST00000572499.1(RPH3AL-AS2):n.225+278_225+279insA variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.97 ( 71264 hom., cov: 0)
Exomes 𝑓: 1.0 ( 5 hom. )
Consequence
RPH3AL-AS2
ENST00000572499.1 intron, non_coding_transcript
ENST00000572499.1 intron, non_coding_transcript
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.999
Genes affected
RPH3AL-AS2 (HGNC:56089): (RPH3AL antisense RNA 2)
RPH3AL (HGNC:10296): (rabphilin 3A like (without C2 domains)) The protein encoded by this gene plays a direct regulatory role in calcium-ion-dependent exocytosis in both endocrine and exocrine cells and plays a key role in insulin secretion by pancreatic cells. This gene is likely a tumor suppressor. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPH3AL-AS2 | ENST00000572499.1 | n.225+278_225+279insA | intron_variant, non_coding_transcript_variant | 3 | |||||
RPH3AL | ENST00000573780.5 | c.-36-25562_-36-25561insT | intron_variant | 4 | |||||
RPH3AL | ENST00000575130.5 | c.-212-19207_-212-19206insT | intron_variant | 4 | |||||
RPH3AL | ENST00000323434.12 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.966 AC: 146995AN: 152112Hom.: 71215 Cov.: 0
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GnomAD4 exome AF: 1.00 AC: 10AN: 10Hom.: 5 Cov.: 0 AF XY: 1.00 AC XY: 8AN XY: 8
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GnomAD4 genome ? AF: 0.966 AC: 147104AN: 152230Hom.: 71264 Cov.: 0 AF XY: 0.967 AC XY: 71978AN XY: 74448
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3478
ClinVar
Not reported inComputational scores
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at