Variant X-140783697-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The ENST00000648200.2(LINC00632):n.11716G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0018 in 1,207,911 control chromosomes in the GnomAD database, including 9 homozygotes. There are 736 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0024 ( 0 hom., 113 hem., cov: 24)

Exomes 𝑓: 0.0017 ( 9 hom. 623 hem. )

Consequence

LINC00632
ENST00000648200.2 non_coding_transcript_exon

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.604

Variant links:

Genes affected

LINC00632 (HGNC:27865): (long intergenic non-protein coding RNA 632)

LINC00632 links:

CDR1 (HGNC:1798): (cerebellar degeneration related 1)

CDR1 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 (MetaRNN=0.0022028089).

BP6

Variant X-140783697-G-A is Benign according to our data. Variant chrX-140783697-G-A is described in ClinVar as [Benign]. Clinvar id is 789465.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-140783697-G-A is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00237 (261/110340) while in subpopulation EAS AF= 0.0292 (100/3422). AF 95% confidence interval is 0.0246. There are 0 homozygotes in gnomad4. There are 113 alleles in male gnomad4 subpopulation. Median coverage is 24. This position pass quality control queck.

BS2

High Hemizygotes in GnomAd4 at 113 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDR1	XR_006652813.2 linkuse as main transcript	n.9516C>T		non_coding_transcript_exon_variant	1/1
LINC00632	NR_173144.1 linkuse as main transcript	n.345-7305G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00632	ENST00000648200.2 linkuse as main transcript	n.11716G>A		non_coding_transcript_exon_variant	5/5
CDR1	ENST00000674533.1 linkuse as main transcript	n.670C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.00237

AC:

261

AN:

110286

Hom.:

Cov.:

AF XY:

0.00344

AC XY:

113

AN XY:

32818

show subpopulations

Gnomad AFR

AF:

0.00116

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000193

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0291

Gnomad SAS

AF:

0.00305

Gnomad FIN

AF:

0.0155

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000455

Gnomad OTH

AF:

0.00134

GnomAD3 exomes

AF:

0.00442

AC:

810

AN:

183213

Hom.:

AF XY:

0.00381

AC XY:

258

AN XY:

67721

show subpopulations

Gnomad AFR exome

AF:

0.000685

Gnomad AMR exome

AF:

0.000146

Gnomad ASJ exome

AF:

0.000134

Gnomad EAS exome

AF:

0.0333

Gnomad SAS exome

AF:

0.00105

Gnomad FIN exome

AF:

0.0150

Gnomad NFE exome

AF:

0.000636

Gnomad OTH exome

AF:

0.00508

GnomAD4 exome

AF:

0.00175

AC:

1919

AN:

1097571

Hom.:

Cov.:

AF XY:

0.00172

AC XY:

623

AN XY:

362991

show subpopulations

Gnomad4 AFR exome

AF:

0.000493

Gnomad4 AMR exome

AF:

0.000284

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0305

Gnomad4 SAS exome

AF:

0.000814

Gnomad4 FIN exome

AF:

0.0144

Gnomad4 NFE exome

AF:

0.000234

Gnomad4 OTH exome

AF:

0.00317

GnomAD4 genome

AF:

0.00237

AC:

261

AN:

110340

Hom.:

Cov.:

AF XY:

0.00344

AC XY:

113

AN XY:

32882

show subpopulations

Gnomad4 AFR

AF:

0.00115

Gnomad4 AMR

AF:

0.000193

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0292

Gnomad4 SAS

AF:

0.00306

Gnomad4 FIN

AF:

0.0155

Gnomad4 NFE

AF:

0.000455

Gnomad4 OTH

AF:

0.00132

Alfa

AF:

0.000808

Hom.:

Bravo

AF:

0.00230

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.00

AC:

ESP6500AA

AF:

0.00104

AC:

ESP6500EA

AF:

0.000149

AC:

ExAC

AF:

0.00428

AC:

519

EpiCase

AF:

0.000109

EpiControl

AF:

0.00

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 07, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.019

FATHMM_MKL

Benign

0.21

LIST_S2

Benign

0.51

MetaRNN

Benign

0.0022

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.0

MutationTaster

Benign

0.83

PrimateAI

Benign

0.23

PROVEAN

Benign

-0.57

REVEL

Benign

0.020

Sift

Uncertain

0.017

Sift4G

Uncertain

0.033

Polyphen

0.0010

Vest4

0.061

MVP

0.23

MPC

0.37

ClinPred

0.016

GERP RS

1.5

Varity_R

0.095

gMVP

0.015

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