Variant 12-123436340-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_145058.3(RILPL2):c.81G>C(p.Gly27Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0089 in 1,565,056 control chromosomes in the GnomAD database, including 86 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0050 ( 7 hom., cov: 32)

Exomes 𝑓: 0.0093 ( 79 hom. )

Consequence

RILPL2
NM_145058.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.482

Variant links:

Genes affected

RILPL2 (HGNC:28787): (Rab interacting lysosomal protein like 2) This gene encodes a protein that contains a rab-interacting lysosomal protein-like domain. This protein may be involved in regulating lysosome morphology. This protein may also be a target for the Hepatitis C virus and assist in viral replication. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

RILPL2 links:

RILPL2 (HGNC:):

RILPL2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 12-123436340-C-G is Benign according to our data. Variant chr12-123436340-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2643510.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.482 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RILPL2	NM_145058.3 linkuse as main transcript	c.81G>C	p.Gly27Gly	synonymous_variant	1/4	ENST00000280571.10	NP_659495.1	Q969X0
RILPL2	XM_047428476.1 linkuse as main transcript	c.81G>C	p.Gly27Gly	synonymous_variant	1/4		XP_047284432.1
RILPL2	XM_011538012.4 linkuse as main transcript	c.81G>C	p.Gly27Gly	synonymous_variant	1/4		XP_011536314.1
RILPL2	NR_130703.2 linkuse as main transcript	n.345G>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RILPL2	ENST00000280571.10 linkuse as main transcript	c.81G>C	p.Gly27Gly	synonymous_variant	1/4	1	NM_145058.3	ENSP00000280571.8		Q969X0

Frequencies

GnomAD3 genomes

AF:

0.00507

AC:

771

AN:

152218

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00150

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00249

Gnomad ASJ

AF:

0.00432

Gnomad EAS

AF:

0.000384

Gnomad SAS

AF:

0.00186

Gnomad FIN

AF:

0.00358

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00878

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00552

AC:

940

AN:

170240

Hom.:

AF XY:

0.00573

AC XY:

519

AN XY:

90574

show subpopulations

Gnomad AFR exome

AF:

0.00134

Gnomad AMR exome

AF:

0.00246

Gnomad ASJ exome

AF:

0.00518

Gnomad EAS exome

AF:

0.0000814

Gnomad SAS exome

AF:

0.00268

Gnomad FIN exome

AF:

0.00524

Gnomad NFE exome

AF:

0.00933

Gnomad OTH exome

AF:

0.00509

GnomAD4 exome

AF:

0.00931

AC:

13153

AN:

1412720

Hom.:

Cov.:

AF XY:

0.00919

AC XY:

6420

AN XY:

698266

show subpopulations

Gnomad4 AFR exome

AF:

0.00140

Gnomad4 AMR exome

AF:

0.00268

Gnomad4 ASJ exome

AF:

0.00509

Gnomad4 EAS exome

AF:

0.0000273

Gnomad4 SAS exome

AF:

0.00262

Gnomad4 FIN exome

AF:

0.00565

Gnomad4 NFE exome

AF:

0.0110

Gnomad4 OTH exome

AF:

0.00780

GnomAD4 genome

AF:

0.00505

AC:

769

AN:

152336

Hom.:

Cov.:

AF XY:

0.00425

AC XY:

317

AN XY:

74504

show subpopulations

Gnomad4 AFR

AF:

0.00149

Gnomad4 AMR

AF:

0.00235

Gnomad4 ASJ

AF:

0.00432

Gnomad4 EAS

AF:

0.000385

Gnomad4 SAS

AF:

0.00186

Gnomad4 FIN

AF:

0.00358

Gnomad4 NFE

AF:

0.00878

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00743

Hom.:

Bravo

AF:

0.00508

Asia WGS

AF:

0.00202

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

RILPL2: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

4.4

DANN

Benign

0.92

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over