Genetic Variant ENST00000625883.2:n.709A>G (chrX-140783796-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000625883.2(LINC00632):n.709A>G 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 0.000121 in 1,207,503 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 53 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00012 ( 0 hom., 4 hem., cov: 24)

Exomes 𝑓: 0.00012 ( 0 hom. 49 hem. )

Consequence

LINC00632
ENST00000625883.2 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.82

Publications

0 publications found

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 was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.03625685).

BP6

Variant X-140783796-A-G is Benign according to our data. Variant chrX-140783796-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 3489720.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 4 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000625883.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC00632	NR_173140.2	MANE Select	n.1073A>G	non_coding_transcript_exon	Exon 5 of 5
LINC00632	NR_173139.1		n.966A>G	non_coding_transcript_exon	Exon 5 of 5
LINC00632	NR_173141.1		n.709A>G	non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC00632	ENST00000649329.2	MANE Select	n.1073A>G	non_coding_transcript_exon	Exon 5 of 5
LINC00632	ENST00000625883.2	TSL:6	n.709A>G	non_coding_transcript_exon	Exon 2 of 2
LINC00632	ENST00000648200.2		n.11815A>G	non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.000125

AC:

AN:

111973

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000946

Gnomad ASJ

AF:

0.000756

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000169

Gnomad OTH

AF:

0.00133

GnomAD2 exomes

AF:

0.000172

AC:

AN:

180475

AF XY:

0.000215

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000222

Gnomad ASJ exome

AF:

0.000417

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000161

Gnomad OTH exome

AF:

0.000453

GnomAD4 exome

AF:

0.000120

AC:

132

AN:

1095478

Hom.:

Cov.:

AF XY:

0.000135

AC XY:

AN XY:

361934

show subpopulations

African (AFR)

AF:

0.0000380

AC:

AN:

26328

American (AMR)

AF:

0.000172

AC:

AN:

34977

Ashkenazi Jewish (ASJ)

AF:

0.000831

AC:

AN:

19261

East Asian (EAS)

AF:

0.00

AC:

AN:

30194

South Asian (SAS)

AF:

0.000280

AC:

AN:

53552

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40477

Middle Eastern (MID)

AF:

0.00388

AC:

AN:

4119

European-Non Finnish (NFE)

AF:

0.0000738

AC:

AN:

840598

Other (OTH)

AF:

0.000348

AC:

AN:

45972

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000125

AC:

AN:

112025

Hom.:

Cov.:

AF XY:

0.000116

AC XY:

AN XY:

34339

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

30924

American (AMR)

AF:

0.0000945

AC:

AN:

10584

Ashkenazi Jewish (ASJ)

AF:

0.000756

AC:

AN:

2647

East Asian (EAS)

AF:

0.00

AC:

AN:

3517

South Asian (SAS)

AF:

0.00

AC:

AN:

2680

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6141

Middle Eastern (MID)

AF:

0.00

AC:

AN:

214

European-Non Finnish (NFE)

AF:

0.000169

AC:

AN:

53112

Other (OTH)

AF:

0.00131

AC:

AN:

1526

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000116

Hom.:

Bravo

AF:

0.000125

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000297

AC:

ExAC

AF:

0.000148

AC:

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.66

CADD

Benign

0.37

(source)

DANN

Benign

0.21

DEOGEN2

Benign

0.033

FATHMM_MKL

Benign

0.030

LIST_S2

Benign

0.21

M_CAP

Benign

0.011

MetaRNN

Benign

0.036

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.34

PhyloP100

-3.8

PrimateAI

Benign

0.24

PROVEAN

Benign

-1.4

REVEL

Benign

0.049

Sift

Benign

0.20

Sift4G

Pathogenic

0.0

Polyphen

0.0010

Vest4

0.11

MutPred

0.69

Gain of sheet (P = 0.0221)

MVP

0.37

MPC

0.44

ClinPred

0.10

GERP RS

-1.1

Varity_R

0.13

gMVP

0.027

Mutation Taster

=99/1

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over