rs9891032

Variant names:

• chr17-353571-A-G
• rs9891032
• ENST00000717666.1:n.958A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000717666.1(RPH3AL-AS2):​n.958A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.24 (203 hom., cov: 0)
• Consequence: RPH3AL-AS2 ENST00000717666.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.306 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.958A>G		non_coding_transcript_exon_variant	Exon 1 of 2
RPH3AL	ENST00000573780.5	c.-36-25992T>C		intron_variant	Intron 1 of 4	4		ENSP00000459992.1
RPH3AL	ENST00000575130.5	c.-212-19637T>C		intron_variant	Intron 1 of 4	4		ENSP00000460171.1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 5807 AN: 24466 Hom.: 199 Cov.: 0

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.238 AC: 5826 AN: 24508 Hom.: 203 Cov.: 0 AF XY: 0.249 AC XY: 2992 AN XY: 11994

African (AFR) AF: 0.268 AC: 3057 AN: 11404

American (AMR) AF: 0.236 AC: 456 AN: 1932

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 71 AN: 438

East Asian (EAS) AF: 0.196 AC: 95 AN: 484

South Asian (SAS) AF: 0.351 AC: 156 AN: 444

European-Finnish (FIN) AF: 0.279 AC: 362 AN: 1298

Middle Eastern (MID) AF: 0.156 AC: 5 AN: 32

European-Non Finnish (NFE) AF: 0.189 AC: 1524 AN: 8050

Other (OTH) AF: 0.221 AC: 72 AN: 326

Alfa AF: 0.473 Hom.: 246

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.22
PhyloP100		0.032
PromoterAI		-0.0023	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9891032; hg19: chr17-203362;