chr17-45729559-G-A

Variant summary

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

The ENST00000634540.1(LINC02210-CRHR1):​c.-492-77451G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,048 control chromosomes in the GnomAD database, including 2,202 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 0.15 ( 2202 hom., cov: 31)

Consequence

LINC02210-CRHR1
ENST00000634540.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.247

Publications

23 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]

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=-0.8).
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-CRHR1NM_001303016.1 linkc.-185+56657G>A intron_variant Intron 3 of 12 NP_001289945.1
LINC02210-CRHR1NM_001256299.3 linkc.-492-77451G>A intron_variant Intron 3 of 14 NP_001243228.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC02210-CRHR1ENST00000634540.1 linkc.-492-77451G>A intron_variant Intron 3 of 14 2 ENSP00000488912.1
LINC02210-CRHR1ENST00000587305.1 linkn.447+56657G>A intron_variant Intron 3 of 4 5

Frequencies

GnomAD3 genomes
AF:
0.150
AC:
22851
AN:
151930
Hom.:
2205
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0666
Gnomad AMI
AF:
0.277
Gnomad AMR
AF:
0.179
Gnomad ASJ
AF:
0.241
Gnomad EAS
AF:
0.00155
Gnomad SAS
AF:
0.0745
Gnomad FIN
AF:
0.0652
Gnomad MID
AF:
0.224
Gnomad NFE
AF:
0.217
Gnomad OTH
AF:
0.192
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.150
AC:
22846
AN:
152048
Hom.:
2202
Cov.:
31
AF XY:
0.141
AC XY:
10468
AN XY:
74344
show subpopulations
African (AFR)
AF:
0.0666
AC:
2764
AN:
41504
American (AMR)
AF:
0.179
AC:
2737
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
0.241
AC:
835
AN:
3464
East Asian (EAS)
AF:
0.00156
AC:
8
AN:
5136
South Asian (SAS)
AF:
0.0745
AC:
359
AN:
4816
European-Finnish (FIN)
AF:
0.0652
AC:
691
AN:
10602
Middle Eastern (MID)
AF:
0.221
AC:
64
AN:
290
European-Non Finnish (NFE)
AF:
0.217
AC:
14738
AN:
67938
Other (OTH)
AF:
0.189
AC:
398
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
951
1902
2853
3804
4755
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
244
488
732
976
1220
<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:
0.197
Hom.:
1917
Bravo
AF:
0.156
Asia WGS
AF:
0.0330
AC:
117
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
12
DANN
Benign
0.85
PhyloP100
0.25
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs2902662; hg19: chr17-43806925; API