rs11356210

chr17-353673-CA-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000572499.1(RPH3AL-AS2):n.225+812del 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 0.089 (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: -0.0560

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 Uncertain_significance. Variant got 0 ACMG points.

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+812del		intron_variant, non_coding_transcript_variant		3
RPH3AL	ENST00000573780.5	c.-36-26095del		intron_variant		4
RPH3AL	ENST00000575130.5	c.-212-19740del		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0894 AC: 2120 AN: 23724 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0497

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0896

Gnomad EAS AF: 0.0526

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0870

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.104

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: 0.0893 AC: 2122 AN: 23764 Hom.: 0 Cov.: 0 AF XY: 0.0916 AC XY: 1067 AN XY: 11648

Gnomad4 AFR AF: 0.0494

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0896

Gnomad4 EAS AF: 0.0541

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.104

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11356210; hg19: chr17-203464; COSMIC: COSV58741242;