17-353673-CA-C

Variant names:

• chr17-353673-CA-C
• rs11356210
• ENST00000717666.1:n.1061delA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000717666.1(RPH3AL-AS2):​n.1061delA variant causes a non coding transcript exon 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 ENST00000717666.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPH3AL-AS2	ENST00000717666.1	n.1061delA		non_coding_transcript_exon_variant	Exon 1 of 2
RPH3AL	ENST00000573780.5	c.-36-26095delT		intron_variant	Intron 1 of 4	4		ENSP00000459992.1
RPH3AL	ENST00000575130.5	c.-212-19740delT		intron_variant	Intron 1 of 4	4		ENSP00000460171.1

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0494 AC: 412 AN: 8334

American (AMR) AF: 0.117 AC: 253 AN: 2166

Ashkenazi Jewish (ASJ) AF: 0.0896 AC: 45 AN: 502

East Asian (EAS) AF: 0.0541 AC: 41 AN: 758

South Asian (SAS) AF: 0.147 AC: 79 AN: 538

European-Finnish (FIN) AF: 0.118 AC: 151 AN: 1280

Middle Eastern (MID) AF: 0.0714 AC: 3 AN: 42

European-Non Finnish (NFE) AF: 0.112 AC: 1087 AN: 9676

Other (OTH) AF: 0.104 AC: 35 AN: 338

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.056

Splicing

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

Other links and lift over

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