Variant rs11869174 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_006987.4(RPH3AL):c.-213+3805A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,146 control chromosomes in the GnomAD database, including 3,639 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 0.21 ( 3638 hom., cov: 32)

Exomes 𝑓: 0.40 ( 1 hom. )

Consequence

RPH3AL
NM_006987.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0810

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
RPH3AL	NM_006987.4 linkuse as main transcript	c.-213+3805A>G	intron_variant	ENST00000331302.12	NP_008918.1
RPH3AL	NM_001190411.2 linkuse as main transcript	c.-37+3805A>G	intron_variant		NP_001177340.1
RPH3AL	NM_001190412.2 linkuse as main transcript	c.-213+3805A>G	intron_variant		NP_001177341.1
RPH3AL	NM_001190413.2 linkuse as main transcript	c.-37+3805A>G	intron_variant		NP_001177342.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPH3AL	ENST00000331302.12 linkuse as main transcript	c.-213+3805A>G		intron_variant		2	NM_006987.4	ENSP00000328977	P1	Q9UNE2-1

Frequencies

GnomAD3 genomes

AF:

0.211

AC:

32037

AN:

152016

Hom.:

3637

Cov.:

show subpopulations

Gnomad AFR

AF:

0.167

Gnomad AMI

AF:

0.192

Gnomad AMR

AF:

0.157

Gnomad ASJ

AF:

0.258

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.223

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.219

GnomAD4 exome

AF:

0.400

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.500

Gnomad4 OTH exome

AF:

0.375

GnomAD4 genome

AF:

0.211

AC:

32056

AN:

152136

Hom.:

3638

Cov.:

AF XY:

0.204

AC XY:

15145

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.167

Gnomad4 AMR

AF:

0.157

Gnomad4 ASJ

AF:

0.258

Gnomad4 EAS

AF:

0.142

Gnomad4 SAS

AF:

0.140

Gnomad4 FIN

AF:

0.207

Gnomad4 NFE

AF:

0.258

Gnomad4 OTH

AF:

0.217

Alfa

AF:

0.250

Hom.:

5851

Bravo

AF:

0.208

Asia WGS

AF:

0.137

AC:

477

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

4.1

DANN

Benign

0.68

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