ENST00000909956.1:c.*88G>C

Variant names:

• chr5-76981013-G-C
• rs1500
• ENST00000909956.1:c.*88G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000909956.1(CRHBP):​c.*88G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,990 control chromosomes in the GnomAD database, including 17,932 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 0.46 (17930 hom., cov: 32)
  • Exomes 𝑓: 0.37 (2 hom.)
• Consequence: CRHBP ENST00000909956.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000909956.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRHBP	ENST00000909956.1		c.*88G>C		3_prime_UTR	Exon 8 of 8	ENSP00000580015.1
	CRHBP	ENST00000514258.1	TSL:3	n.520G>C		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69658 AN: 151842 Hom.: 17897 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.457

GnomAD4 exome AF: 0.367 AC: 11 AN: 30 Hom.: 2 Cov.: 0 AF XY: 0.389 AC XY: 7 AN XY: 18

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.385 AC: 10 AN: 26

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.459 AC: 69740 AN: 151960 Hom.: 17930 Cov.: 32 AF XY: 0.460 AC XY: 34153 AN XY: 74282

African (AFR) AF: 0.696 AC: 28855 AN: 41444

American (AMR) AF: 0.365 AC: 5577 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1334 AN: 3462

East Asian (EAS) AF: 0.583 AC: 3007 AN: 5160

South Asian (SAS) AF: 0.421 AC: 2027 AN: 4814

European-Finnish (FIN) AF: 0.427 AC: 4498 AN: 10544

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.339 AC: 23039 AN: 67952

Other (OTH) AF: 0.459 AC: 971 AN: 2116

Alfa AF: 0.230 Hom.: 485

Bravo AF: 0.464

Asia WGS AF: 0.510 AC: 1777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.42
DANN	Benign	0.44
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1500; hg19: chr5-76276838;