Variant rs4985615 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006987.4(RPH3AL):c.78-1144C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,034 control chromosomes in the GnomAD database, including 7,099 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 0.30 ( 7099 hom., cov: 32)

Exomes 𝑓: 0.23 ( 0 hom. )

Consequence

RPH3AL
NM_006987.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.87

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
RPH3AL	NM_006987.4 link	c.78-1144C>G	intron_variant	ENST00000331302.12	NP_008918.1	Q9UNE2-1
RPH3AL	NM_001190411.2 link	c.78-1144C>G	intron_variant		NP_001177340.1	Q9UNE2-1
RPH3AL	NM_001190412.2 link	c.78-1144C>G	intron_variant		NP_001177341.1	Q9UNE2-2A8K7D5
RPH3AL	NM_001190413.2 link	c.78-1144C>G	intron_variant		NP_001177342.1	Q9UNE2-2A8K7D5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPH3AL	ENST00000331302.12 link	c.78-1144C>G		intron_variant		2	NM_006987.4	ENSP00000328977.7		Q9UNE2-1

Frequencies

GnomAD3 genomes

AF:

0.304

AC:

46100

AN:

151890

Hom.:

7099

Cov.:

show subpopulations

Gnomad AFR

AF:

0.316

Gnomad AMI

AF:

0.364

Gnomad AMR

AF:

0.323

Gnomad ASJ

AF:

0.266

Gnomad EAS

AF:

0.430

Gnomad SAS

AF:

0.315

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.296

GnomAD4 exome

AF:

0.231

AC:

AN:

Hom.:

AF XY:

0.143

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.300

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.303

AC:

46116

AN:

152008

Hom.:

7099

Cov.:

AF XY:

0.305

AC XY:

22646

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.316

Gnomad4 AMR

AF:

0.323

Gnomad4 ASJ

AF:

0.266

Gnomad4 EAS

AF:

0.429

Gnomad4 SAS

AF:

0.315

Gnomad4 FIN

AF:

0.264

Gnomad4 NFE

AF:

0.288

Gnomad4 OTH

AF:

0.294

Alfa

AF:

0.166

Hom.:

321

Bravo

AF:

0.309

Asia WGS

AF:

0.390

AC:

1359

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.34

DANN

Benign

0.57

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over