ENST00000573780.5:c.-36-25963delT

Variant names:

• chr17-353541-CA-C
• rs11356209
• ENST00000573780.5:c.-36-25963delT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000573780.5(RPH3AL):​c.-36-25963delT variant causes a intron 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 ENST00000573780.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.517

Genes affected

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]

RPH3AL-AS2 (HGNC:56089): (RPH3AL antisense RNA 2)

ACMG classification

Verdict is Benign. Variant got -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	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
RPH3AL-AS2	ENST00000572499.1	n.225+680delA		intron_variant	Intron 1 of 1	3

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

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.495

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