rs12942009

Positions:

• chr17-353665-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000572499.1(RPH3AL-AS2):​n.225+803C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.16 (0 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: RPH3AL-AS2 ENST00000572499.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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+803C>T		intron_variant, non_coding_transcript_variant		3
RPH3AL	ENST00000573780.5	c.-36-26086G>A		intron_variant		4
RPH3AL	ENST00000575130.5	c.-212-19731G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 3122 AN: 20070 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0818

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.181

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.155 AC: 3125 AN: 20104 Hom.: 0 Cov.: 0 AF XY: 0.160 AC XY: 1580 AN XY: 9852

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0831

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.181

Alfa AF: 0.419 Hom.: 168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.6
DANN	Benign	0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12942009; hg19: chr17-203456;