rs241031

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001303016.1(LINC02210-CRHR1):​c.-260-15889T>C 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 152,240 control chromosomes in the GnomAD database, including 2,146 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 ( 2146 hom., cov: 32)

Consequence

LINC02210-CRHR1
NM_001303016.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.652
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
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/exons MANE Protein UniProt
LINC02210-CRHR1NM_001303016.1 linkuse as main transcriptc.-260-15889T>C intron_variant NP_001289945.1
LINC02210-CRHR1NM_001256299.3 linkuse as main transcriptc.-493+26780T>C intron_variant NP_001243228.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02210-CRHR1ENST00000634540.1 linkuse as main transcriptc.-493+26780T>C intron_variant 2 ENSP00000488912.1
LINC02210-CRHR1ENST00000587305.1 linkuse as main transcriptn.372-15889T>C intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.144
AC:
21858
AN:
152122
Hom.:
2148
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0431
Gnomad AMI
AF:
0.315
Gnomad AMR
AF:
0.176
Gnomad ASJ
AF:
0.240
Gnomad EAS
AF:
0.00154
Gnomad SAS
AF:
0.0742
Gnomad FIN
AF:
0.0650
Gnomad MID
AF:
0.222
Gnomad NFE
AF:
0.217
Gnomad OTH
AF:
0.186
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.144
AC:
21848
AN:
152240
Hom.:
2146
Cov.:
32
AF XY:
0.134
AC XY:
10000
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.0430
Gnomad4 AMR
AF:
0.176
Gnomad4 ASJ
AF:
0.240
Gnomad4 EAS
AF:
0.00154
Gnomad4 SAS
AF:
0.0742
Gnomad4 FIN
AF:
0.0650
Gnomad4 NFE
AF:
0.217
Gnomad4 OTH
AF:
0.183
Alfa
AF:
0.193
Hom.:
1293
Bravo
AF:
0.149
Asia WGS
AF:
0.0310
AC:
110
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.81
DANN
Benign
0.25

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.

Other links and lift over

dbSNP: rs241031; hg19: chr17-43734304; API