Variant 12-123533434-TCTCCAGCGCCGACTCGGC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PM4PP3BP6BS2

The ENST00000376874.9(RILPL1):c.31_48delGCCGAGTCGGCGCTGGAG(p.Ala11_Glu16del) variant causes a conservative inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000169 in 1,537,202 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00016 ( 1 hom., cov: 32)

Exomes 𝑓: 0.00017 ( 1 hom. )

Consequence

RILPL1
ENST00000376874.9 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 7.68

Variant links:

Genes affected

RILPL1 (HGNC:26814): (Rab interacting lysosomal protein like 1) Predicted to enable protein dimerization activity. Predicted to be involved in several processes, including cilium assembly; epithelial cell morphogenesis; and protein transport from ciliary membrane to plasma membrane. Located in cytosol; nucleoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

RILPL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in ENST00000376874.9.

PP3

No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

BP6

Variant 12-123533434-TCTCCAGCGCCGACTCGGC-T is Benign according to our data. Variant chr12-123533434-TCTCCAGCGCCGACTCGGC-T is described in ClinVar as [Likely_benign]. Clinvar id is 2681516.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High AC in GnomAd4 at 24 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RILPL1	NM_178314.5 linkuse as main transcript	c.31_48delGCCGAGTCGGCGCTGGAG	p.Ala11_Glu16del	conservative_inframe_deletion	1/7	ENST00000376874.9	NP_847884.2	Q5EBL4-1
RILPL1	NM_001319243.2 linkuse as main transcript	c.31_48delGCCGAGTCGGCGCTGGAG	p.Ala11_Glu16del	conservative_inframe_deletion	1/8		NP_001306172.1	Q5EBL4A0A1B0GVV3
RILPL1	XM_047428787.1 linkuse as main transcript	c.31_48delGCCGAGTCGGCGCTGGAG	p.Ala11_Glu16del	conservative_inframe_deletion	1/7		XP_047284743.1
RILPL1	XM_047428788.1 linkuse as main transcript	c.31_48delGCCGAGTCGGCGCTGGAG	p.Ala11_Glu16del	conservative_inframe_deletion	1/3		XP_047284744.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RILPL1	ENST00000376874.9 linkuse as main transcript	c.31_48delGCCGAGTCGGCGCTGGAG	p.Ala11_Glu16del	conservative_inframe_deletion	1/7	1	NM_178314.5	ENSP00000366070.4		Q5EBL4-1
RILPL1	ENST00000636882.1 linkuse as main transcript	c.31_48delGCCGAGTCGGCGCTGGAG	p.Ala11_Glu16del	conservative_inframe_deletion	1/8	5		ENSP00000490668.1		A0A1B0GVV3

Frequencies

GnomAD3 genomes

AF:

0.000158

AC:

AN:

152012

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00232

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000162

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000493

AC:

AN:

140080

Hom.:

AF XY:

0.000566

AC XY:

AN XY:

75936

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00523

Gnomad SAS exome

AF:

0.000223

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000137

Gnomad OTH exome

AF:

0.000242

GnomAD4 exome

AF:

0.000170

AC:

236

AN:

1385072

Hom.:

AF XY:

0.000178

AC XY:

121

AN XY:

681090

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00311

Gnomad4 SAS exome

AF:

0.000177

Gnomad4 FIN exome

AF:

0.0000226

Gnomad4 NFE exome

AF:

0.0000849

Gnomad4 OTH exome

AF:

0.000349

GnomAD4 genome

AF:

0.000158

AC:

AN:

152130

Hom.:

Cov.:

AF XY:

0.000161

AC XY:

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00232

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000162

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000145

Hom.:

Bravo

AF:

0.000204

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

EBV-positive nodal T- and NK-cell lymphoma

Benign:1

Likely benign, no assertion criteria provided

research

Department of Clinical Pathology, School of Medicine, Fujita Health University

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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