Variant rs17689966 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_004382.5(CRHR1):c.771-49G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 1,513,444 control chromosomes in the GnomAD database, including 271,848 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 0.56 ( 24827 hom., cov: 33)

Exomes 𝑓: 0.60 ( 247021 hom. )

Consequence

CRHR1
NM_004382.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.34

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]

CRHR1 links:

LINC02210-CRHR1 (HGNC:):

LINC02210-CRHR1 links:

MAPT-AS1 (HGNC:43738): (MAPT antisense RNA 1) Implicated in Parkinson's disease. [provided by Alliance of Genome Resources, Apr 2022]

MAPT-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRHR1	NM_004382.5 linkuse as main transcript	c.771-49G>A		intron_variant		ENST00000314537.10	NP_004373.2
LINC02210-CRHR1	NM_001256299.3 linkuse as main transcript	c.246-49G>A		intron_variant			NP_001243228.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRHR1	ENST00000314537.10 linkuse as main transcript	c.771-49G>A		intron_variant		1	NM_004382.5	ENSP00000326060	P1	P34998-2
MAPT-AS1	ENST00000634876.2 linkuse as main transcript	n.604-3728C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.564

AC:

85683

AN:

151948

Hom.:

24823

Cov.:

show subpopulations

Gnomad AFR

AF:

0.461

Gnomad AMI

AF:

0.596

Gnomad AMR

AF:

0.614

Gnomad ASJ

AF:

0.540

Gnomad EAS

AF:

0.813

Gnomad SAS

AF:

0.765

Gnomad FIN

AF:

0.708

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.561

Gnomad OTH

AF:

0.544

GnomAD3 exomes

AF:

0.634

AC:

157777

AN:

248734

Hom.:

51546

AF XY:

0.636

AC XY:

85850

AN XY:

134940

show subpopulations

Gnomad AFR exome

AF:

0.450

Gnomad AMR exome

AF:

0.714

Gnomad ASJ exome

AF:

0.535

Gnomad EAS exome

AF:

0.814

Gnomad SAS exome

AF:

0.766

Gnomad FIN exome

AF:

0.712

Gnomad NFE exome

AF:

0.566

Gnomad OTH exome

AF:

0.608

GnomAD4 exome

AF:

0.598

AC:

813548

AN:

1361378

Hom.:

247021

Cov.:

AF XY:

0.602

AC XY:

411005

AN XY:

683066

show subpopulations

Gnomad4 AFR exome

AF:

0.446

Gnomad4 AMR exome

AF:

0.705

Gnomad4 ASJ exome

AF:

0.529

Gnomad4 EAS exome

AF:

0.819

Gnomad4 SAS exome

AF:

0.765

Gnomad4 FIN exome

AF:

0.702

Gnomad4 NFE exome

AF:

0.572

Gnomad4 OTH exome

AF:

0.599

GnomAD4 genome

AF:

0.564

AC:

85706

AN:

152066

Hom.:

24827

Cov.:

AF XY:

0.576

AC XY:

42794

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.460

Gnomad4 AMR

AF:

0.615

Gnomad4 ASJ

AF:

0.540

Gnomad4 EAS

AF:

0.812

Gnomad4 SAS

AF:

0.766

Gnomad4 FIN

AF:

0.708

Gnomad4 NFE

AF:

0.561

Gnomad4 OTH

AF:

0.545

Alfa

AF:

0.556

Hom.:

20672

Bravo

AF:

0.551

Asia WGS

AF:

0.753

AC:

2618

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.56

DANN

Benign

0.34

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over