Variant rs4151551 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001162498.3(LPAR6):c.*86C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0729 in 1,087,814 control chromosomes in the GnomAD database, including 3,440 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.058 ( 361 hom., cov: 32)

Exomes 𝑓: 0.075 ( 3079 hom. )

Consequence

LPAR6
NM_001162498.3 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.128

Variant links:

Genes affected

LPAR6 (HGNC:15520): (lysophosphatidic acid receptor 6) The protein encoded by this gene belongs to the family of G-protein coupled receptors, that are preferentially activated by adenosine and uridine nucleotides. This gene aligns with an internal intron of the retinoblastoma susceptibility gene in the reverse orientation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2009]

LPAR6 links:

RB1 (HGNC:9884): (RB transcriptional corepressor 1) The protein encoded by this gene is a negative regulator of the cell cycle and was the first tumor suppressor gene found. The encoded protein also stabilizes constitutive heterochromatin to maintain the overall chromatin structure. The active, hypophosphorylated form of the protein binds transcription factor E2F1. Defects in this gene are a cause of childhood cancer retinoblastoma (RB), bladder cancer, and osteogenic sarcoma. [provided by RefSeq, Jul 2008]

RB1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

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

BP6

Variant 13-48411303-G-T is Benign according to our data. Variant chr13-48411303-G-T is described in ClinVar as [Benign]. Clinvar id is 1234731.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPAR6	NM_001162498.3 link	c.*86C>A		3_prime_UTR_variant	Exon 1 of 1	ENST00000620633.5	NP_001155970.1	P43657A0A024RDT2B3KVQ5
RB1	NM_000321.3 link	c.1695+29860G>T		intron_variant	Intron 17 of 26	ENST00000267163.6	NP_000312.2	P06400A0A024RDV3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPAR6	ENST00000620633 link	c.*86C>A		3_prime_UTR_variant	Exon 1 of 1	5	NM_001162498.3	ENSP00000482660.1		P43657
RB1	ENST00000267163.6 link	c.1695+29860G>T		intron_variant	Intron 17 of 26	1	NM_000321.3	ENSP00000267163.4		P06400

Frequencies

GnomAD3 genomes

AF:

0.0583

AC:

8861

AN:

152100

Hom.:

361

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0166

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.0554

Gnomad ASJ

AF:

0.0867

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0151

Gnomad FIN

AF:

0.0423

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0913

Gnomad OTH

AF:

0.0777

GnomAD4 exome

AF:

0.0753

AC:

70425

AN:

935596

Hom.:

3079

Cov.:

AF XY:

0.0740

AC XY:

36119

AN XY:

487826

show subpopulations

Gnomad4 AFR exome

AF:

0.0140

Gnomad4 AMR exome

AF:

0.0443

Gnomad4 ASJ exome

AF:

0.0895

Gnomad4 EAS exome

AF:

0.000134

Gnomad4 SAS exome

AF:

0.0173

Gnomad4 FIN exome

AF:

0.0492

Gnomad4 NFE exome

AF:

0.0924

Gnomad4 OTH exome

AF:

0.0675

GnomAD4 genome

AF:

0.0582

AC:

8853

AN:

152218

Hom.:

361

Cov.:

AF XY:

0.0539

AC XY:

4013

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.0166

Gnomad4 AMR

AF:

0.0552

Gnomad4 ASJ

AF:

0.0867

Gnomad4 EAS

AF:

0.000578

Gnomad4 SAS

AF:

0.0149

Gnomad4 FIN

AF:

0.0423

Gnomad4 NFE

AF:

0.0913

Gnomad4 OTH

AF:

0.0764

Alfa

AF:

0.0780

Hom.:

152

Bravo

AF:

0.0572

Asia WGS

AF:

0.0100

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

May 16, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

DANN

Benign

0.73

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