rs28687962

Variant names:

• chr17-353740-G-A
• rs28687962
• ENST00000907490.1:c.-154-4365C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-353740-G-A
• chr17-353740-G-C
• chr17-353740-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000573780.5(RPH3AL):​c.-36-26161C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000646 in 123,910 control chromosomes in the GnomAD database, including 1 homozygotes. 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 0.000065 (1 hom., cov: 31)
• Consequence: RPH3AL ENST00000573780.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 2 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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.-154-4365C>T		intron	N/A	ENSP00000577549.1
	RPH3AL	ENST00000907489.1		c.-36-26161C>T		intron	N/A	ENSP00000577548.1
	RPH3AL	ENST00000913661.1		c.-153-25912C>T		intron	N/A	ENSP00000583720.1

Frequencies

GnomAD3 genomes AF: 0.0000646 AC: 8 AN: 123910 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000340

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000734

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000646 AC: 8 AN: 123910 Hom.: 1 Cov.: 31 AF XY: 0.0000662 AC XY: 4 AN XY: 60400

African (AFR) AF: 0.00 AC: 0 AN: 35720

American (AMR) AF: 0.000340 AC: 4 AN: 11776

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2722

East Asian (EAS) AF: 0.00 AC: 0 AN: 4340

South Asian (SAS) AF: 0.00 AC: 0 AN: 3706

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8386

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 244

European-Non Finnish (NFE) AF: 0.0000734 AC: 4 AN: 54528

Other (OTH) AF: 0.00 AC: 0 AN: 1716

Alfa AF: 0.00 Hom.: 1995

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.93
PhyloP100		-0.67

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: rs28687962;

hg19: chr17-203531;