rs11356210

Variant names:

• chr17-353673-CA-C
• rs11356210
• ENST00000907490.1:c.-154-4299delT

Variant summary

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

The ENST00000573780.5(RPH3AL):​c.-36-26095delT 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 0.089 (0 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: RPH3AL ENST00000573780.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 0 publications found

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000573780.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPH3AL	ENST00000907490.1		c.-154-4299delT		intron	N/A	ENSP00000577549.1
	RPH3AL	ENST00000907489.1		c.-36-26095delT		intron	N/A	ENSP00000577548.1
	RPH3AL	ENST00000913661.1		c.-153-25846delT		intron	N/A	ENSP00000583720.1

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.056

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11356210;

hg19: chr17-203464;

COSMIC: COSV58741242;