Genetic Variant LINC02210-CRHR1:c.-493+21908C>T (chr17-45652066-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000634540.1(LINC02210-CRHR1):c.-493+21908C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 151,914 control chromosomes in the GnomAD database, including 2,148 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.14 ( 2148 hom., cov: 32)

Exomes 𝑓: 0.11 ( 0 hom. )

Consequence

LINC02210-CRHR1
ENST00000634540.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.153

Publications

17 publications found

Variant links:

Genes affected

LINC02210-CRHR1 (HGNC:51483): (LINC02210-CRHR1 readthrough) This locus represents naturally occurring readthrough transcription between neighboring genes CRHR1-IT1, CRHR1 intronic transcript 1 (Gene ID: 147081) and CRHR1, corticotropin releasing hormone receptor 1 (Gene ID: 1394) on chromosome 17. The readthrough transcript encodes a protein that shares sequence identity with the product of the CRHR1 gene. [provided by RefSeq, Dec 2016]

LINC02210-CRHR1 links:

LINC02210 (HGNC:):

LINC02210 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02210-CRHR1	NM_001303016.1 link	c.-260-20761C>T		intron_variant	Intron 2 of 12		NP_001289945.1
LINC02210-CRHR1	NM_001256299.3 link	c.-493+21908C>T		intron_variant	Intron 3 of 14		NP_001243228.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein
LINC02210-CRHR1	ENST00000634540.1 link	c.-493+21908C>T	intron_variant	Intron 3 of 14	2	ENSP00000488912.1
LINC02210	ENST00000591271.5 link	n.6588C>T	non_coding_transcript_exon_variant	Exon 4 of 4	3
LINC02210-CRHR1	ENST00000587305.1 link	n.372-20761C>T	intron_variant	Intron 2 of 4	5
ENSG00000306349	ENST00000817145.1 link	n.294-2263G>A	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.144

AC:

21855

AN:

151750

Hom.:

2150

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0431

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.177

Gnomad ASJ

AF:

0.240

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.0743

Gnomad FIN

AF:

0.0655

Gnomad MID

AF:

0.223

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.186

GnomAD4 exome

AF:

0.109

AC:

AN:

Hom.:

Cov.:

AF XY:

0.133

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0455

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.188

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.565

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.144

AC:

21845

AN:

151868

Hom.:

2148

Cov.:

AF XY:

0.135

AC XY:

10002

AN XY:

74224

show subpopulations

African (AFR)

AF:

0.0430

AC:

1780

AN:

41400

American (AMR)

AF:

0.177

AC:

2698

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.240

AC:

831

AN:

3468

East Asian (EAS)

AF:

0.00155

AC:

AN:

5176

South Asian (SAS)

AF:

0.0743

AC:

357

AN:

4804

European-Finnish (FIN)

AF:

0.0655

AC:

691

AN:

10546

Middle Eastern (MID)

AF:

0.219

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.217

AC:

14743

AN:

67920

Other (OTH)

AF:

0.183

AC:

386

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

923

1846

2769

3692

4615

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

234

468

702

936

1170

<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:

0.187

Hom.:

1051

Bravo

AF:

0.149

Asia WGS

AF:

0.0310

AC:

108

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.7

(source)

DANN

Benign

0.66

PhyloP100

-0.15

Mutation Taster

=100/0

polymorphism (auto)

(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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over