rs11356209

Variant names:

• chr17-353541-CA-C
• rs11356209
• ENST00000717666.1:n.929delA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000717666.1(RPH3AL-AS2):​n.929delA 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 0.53 (7236 hom., cov: 0)
• Consequence: RPH3AL-AS2 ENST00000717666.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.517
• 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: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

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.929delA		non_coding_transcript_exon_variant	Exon 1 of 2
RPH3AL	ENST00000573780.5	c.-36-25963delT		intron_variant	Intron 1 of 4	4		ENSP00000459992.1
RPH3AL	ENST00000575130.5	c.-212-19608delT		intron_variant	Intron 1 of 4	4		ENSP00000460171.1

Frequencies

GnomAD3 genomes AF: 0.533 AC: 29132 AN: 54690 Hom.: 7229 Cov.: 0

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.533 AC: 29175 AN: 54770 Hom.: 7236 Cov.: 0 AF XY: 0.543 AC XY: 14748 AN XY: 27144

African (AFR) AF: 0.578 AC: 13514 AN: 23382

American (AMR) AF: 0.566 AC: 2713 AN: 4794

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 522 AN: 1100

East Asian (EAS) AF: 0.709 AC: 1812 AN: 2556

South Asian (SAS) AF: 0.566 AC: 619 AN: 1094

European-Finnish (FIN) AF: 0.578 AC: 2115 AN: 3662

Middle Eastern (MID) AF: 0.521 AC: 50 AN: 96

European-Non Finnish (NFE) AF: 0.430 AC: 7365 AN: 17134

Other (OTH) AF: 0.495 AC: 368 AN: 744

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.52
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11356209; hg19: chr17-203332; COSMIC: COSV58738462;