Variant 19-10321123-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_133452.3(RAVER1):c.1398C>A(p.Pro466Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 1,305,428 control chromosomes in the GnomAD database, including 35,174 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.24 ( 4567 hom., cov: 33)

Exomes 𝑓: 0.23 ( 30607 hom. )

Consequence

RAVER1
NM_133452.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.58

Variant links:

Genes affected

RAVER1 (HGNC:30296): (ribonucleoprotein, PTB binding 1) Enables RNA binding activity. Predicted to be involved in regulation of alternative mRNA splicing, via spliceosome. Predicted to be located in cytoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

RAVER1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 19-10321123-G-T is Benign according to our data. Variant chr19-10321123-G-T is described in ClinVar as [Benign]. Clinvar id is 1245942.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.58 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAVER1	NM_133452.3 linkuse as main transcript	c.1398C>A	p.Pro466Pro	synonymous_variant	8/13	ENST00000617231.5	NP_597709.3	Q8IY67

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
RAVER1	ENST00000617231.5 linkuse as main transcript	c.1398C>A	p.Pro466Pro	synonymous_variant	8/13	5	NM_133452.3	ENSP00000482277.1	A0A087WZ13
RAVER1	ENST00000592208.5 linkuse as main transcript	n.2632C>A		non_coding_transcript_exon_variant	5/10	1
RAVER1	ENST00000585935.5 linkuse as main transcript	n.40C>A		non_coding_transcript_exon_variant	1/5	3
RAVER1	ENST00000593136.2 linkuse as main transcript	n.197-172C>A		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

36333

AN:

151914

Hom.:

4564

Cov.:

show subpopulations

Gnomad AFR

AF:

0.281

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.173

Gnomad ASJ

AF:

0.207

Gnomad EAS

AF:

0.0901

Gnomad SAS

AF:

0.207

Gnomad FIN

AF:

0.259

Gnomad MID

AF:

0.296

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.230

GnomAD3 exomes

AF:

0.297

AC:

2312

AN:

7784

Hom.:

346

AF XY:

0.306

AC XY:

1225

AN XY:

4006

show subpopulations

Gnomad AFR exome

AF:

0.325

Gnomad AMR exome

AF:

0.134

Gnomad ASJ exome

AF:

0.313

Gnomad EAS exome

AF:

0.171

Gnomad SAS exome

AF:

0.256

Gnomad FIN exome

AF:

0.332

Gnomad NFE exome

AF:

0.259

Gnomad OTH exome

AF:

0.298

GnomAD4 exome

AF:

0.227

AC:

261284

AN:

1153396

Hom.:

30607

Cov.:

AF XY:

0.227

AC XY:

124836

AN XY:

550388

show subpopulations

Gnomad4 AFR exome

AF:

0.294

Gnomad4 AMR exome

AF:

0.142

Gnomad4 ASJ exome

AF:

0.215

Gnomad4 EAS exome

AF:

0.0717

Gnomad4 SAS exome

AF:

0.190

Gnomad4 FIN exome

AF:

0.270

Gnomad4 NFE exome

AF:

0.230

Gnomad4 OTH exome

AF:

0.219

GnomAD4 genome

AF:

0.239

AC:

36357

AN:

152032

Hom.:

4567

Cov.:

AF XY:

0.238

AC XY:

17688

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.281

Gnomad4 AMR

AF:

0.173

Gnomad4 ASJ

AF:

0.207

Gnomad4 EAS

AF:

0.0898

Gnomad4 SAS

AF:

0.206

Gnomad4 FIN

AF:

0.259

Gnomad4 NFE

AF:

0.242

Gnomad4 OTH

AF:

0.233

Alfa

AF:

0.158

Hom.:

374

Bravo

AF:

0.231

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 23, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.099

DANN

Benign

0.42

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

3.2

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over