rs10473984

chr5-76971301-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000514258.1(CRHBP):n.312-5064G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,202 control chromosomes in the GnomAD database, including 2,016 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 0.11 (2016 hom., cov: 32)
• Consequence: CRHBP ENST00000514258.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

Genes affected

CRHBP (HGNC:2356): (corticotropin releasing hormone binding protein) Corticotropin-releasing hormone is a potent stimulator of synthesis and secretion of preopiomelanocortin-derived peptides. Although CRH concentrations in the human peripheral circulation are normally low, they increase throughout pregnancy and fall rapidly after parturition. Maternal plasma CRH probably originates from the placenta. Human plasma contains a CRH-binding protein which inactivates CRH and which may prevent inappropriate pituitary-adrenal stimulation in pregnancy. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRHBP	XR_948235.4	n.902-5064G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRHBP	ENST00000514258.1	n.312-5064G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17152 AN: 152084 Hom.: 2010 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0642

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0277

Gnomad FIN AF: 0.0237

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0404

Gnomad OTH AF: 0.111

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.113 AC: 17190 AN: 152202 Hom.: 2016 Cov.: 32 AF XY: 0.108 AC XY: 8072 AN XY: 74422

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.0642

Gnomad4 ASJ AF: 0.0948

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0280

Gnomad4 FIN AF: 0.0237

Gnomad4 NFE AF: 0.0403

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0715 Hom.: 342

Bravo AF: 0.127

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.77
Dann	Benign	0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10473984; hg19: chr5-76267126;