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GeneBe

rs110402

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_004382.5(CRHR1):c.34-4329G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,990 control chromosomes in the GnomAD database, including 16,858 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 0.45 ( 16858 hom., cov: 32)

Consequence

CRHR1
NM_004382.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.16
Variant links:
Genes affected
CRHR1 (HGNC:2357): (corticotropin releasing hormone receptor 1) This gene encodes a G-protein coupled receptor that binds neuropeptides of the corticotropin releasing hormone family that are major regulators of the hypothalamic-pituitary-adrenal pathway. The encoded protein is essential for the activation of signal transduction pathways that regulate diverse physiological processes including stress, reproduction, immune response and obesity. Alternative splicing results in multiple transcript variants. Naturally-occurring readthrough transcription between this gene and upstream GeneID:147081 results in transcripts that encode isoforms that share similarity with the products of this gene. [provided by RefSeq, Aug 2016]
MAPT-AS1 (HGNC:43738): (MAPT antisense RNA 1) Implicated in Parkinson's disease. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.2).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CRHR1NM_004382.5 linkuse as main transcriptc.34-4329G>A intron_variant ENST00000314537.10
LINC02210-CRHR1NM_001256299.3 linkuse as main transcriptc.-492-4329G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CRHR1ENST00000314537.10 linkuse as main transcriptc.34-4329G>A intron_variant 1 NM_004382.5 P1P34998-2
MAPT-AS1ENST00000634876.2 linkuse as main transcriptn.2594-1891C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.452
AC:
68615
AN:
151872
Hom.:
16854
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.311
Gnomad AMI
AF:
0.476
Gnomad AMR
AF:
0.530
Gnomad ASJ
AF:
0.443
Gnomad EAS
AF:
0.897
Gnomad SAS
AF:
0.699
Gnomad FIN
AF:
0.624
Gnomad MID
AF:
0.383
Gnomad NFE
AF:
0.442
Gnomad OTH
AF:
0.446
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.452
AC:
68631
AN:
151990
Hom.:
16858
Cov.:
32
AF XY:
0.468
AC XY:
34781
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.311
Gnomad4 AMR
AF:
0.531
Gnomad4 ASJ
AF:
0.443
Gnomad4 EAS
AF:
0.897
Gnomad4 SAS
AF:
0.700
Gnomad4 FIN
AF:
0.624
Gnomad4 NFE
AF:
0.442
Gnomad4 OTH
AF:
0.449
Alfa
AF:
0.440
Hom.:
28129
Bravo
AF:
0.438
Asia WGS
AF:
0.747
AC:
2597
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.20
Cadd
Benign
19
Dann
Benign
0.77

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: rs110402; hg19: chr17-43880047; API