NM_000756.4:c.-14-144A>C

Variant names:

• chr8-66177635-T-G
• rs28364018
• NM_000756.4:c.-14-144A>C

Variant summary

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

The NM_000756.4(CRH):​c.-14-144A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.04 in 1,210,714 control chromosomes in the GnomAD database, including 1,105 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 0.040 (158 hom., cov: 32)
  • Exomes 𝑓: 0.040 (947 hom.)
• Consequence: CRH NM_000756.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.16
• Publications: 2 publications found

Genes affected

CRH (HGNC:2355): (corticotropin releasing hormone) This gene encodes a member of the corticotropin-releasing factor family. The encoded preproprotein is proteolytically processed to generate the mature neuropeptide hormone. In response to stress, this hormone is secreted by the paraventricular nucleus (PVN) of the hypothalamus, binds to corticotropin releasing hormone receptors and stimulates the release of adrenocorticotropic hormone from the pituitary gland. Marked reduction in this protein has been observed in association with Alzheimer's disease. Autosomal recessive hypothalamic corticotropin deficiency has multiple and potentially fatal metabolic consequences including hypoglycemia and hepatitis. In addition to production in the hypothalamus, this protein is also synthesized in peripheral tissues, such as T lymphocytes, and is highly expressed in the placenta. In the placenta it is a marker that determines the length of gestation and the timing of parturition and delivery. A rapid increase in circulating levels of the hormone occurs at the onset of parturition, suggesting that, in addition to its metabolic functions, this protein may act as a trigger for parturition. [provided by RefSeq, Nov 2015]

LINC00967 (HGNC:48725): (long intergenic non-protein coding RNA 967)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0561 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000756.4. 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
	CRH	NM_000756.4	MANE Select	c.-14-144A>C		intron	N/A	NP_000747.1	A0A0S2Z478

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRH	ENST00000276571.5	TSL:1 MANE Select	c.-14-144A>C		intron	N/A	ENSP00000276571.3	P06850
	CRH	ENST00000948625.1		c.-14-144A>C		intron	N/A	ENSP00000618684.1
	LINC00967	ENST00000729586.1		n.243+131T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0402 AC: 6110 AN: 152056 Hom.: 158 Cov.: 32

Gnomad AFR AF: 0.0360

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0427

Gnomad ASJ AF: 0.0528

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.00850

Gnomad FIN AF: 0.0252

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.0431

GnomAD4 exome AF: 0.0400 AC: 42370 AN: 1058542 Hom.: 947 AF XY: 0.0395 AC XY: 20502 AN XY: 519652

African (AFR) AF: 0.0318 AC: 668 AN: 20984

American (AMR) AF: 0.0328 AC: 552 AN: 16844

Ashkenazi Jewish (ASJ) AF: 0.0464 AC: 778 AN: 16780

East Asian (EAS) AF: 0.00809 AC: 248 AN: 30670

South Asian (SAS) AF: 0.0103 AC: 581 AN: 56322

European-Finnish (FIN) AF: 0.0185 AC: 547 AN: 29570

Middle Eastern (MID) AF: 0.0633 AC: 198 AN: 3126

European-Non Finnish (NFE) AF: 0.0441 AC: 37018 AN: 838594

Other (OTH) AF: 0.0390 AC: 1780 AN: 45652

GnomAD4 genome AF: 0.0402 AC: 6115 AN: 152172 Hom.: 158 Cov.: 32 AF XY: 0.0393 AC XY: 2923 AN XY: 74416

African (AFR) AF: 0.0361 AC: 1498 AN: 41516

American (AMR) AF: 0.0427 AC: 653 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0528 AC: 183 AN: 3468

East Asian (EAS) AF: 0.0143 AC: 74 AN: 5166

South Asian (SAS) AF: 0.00851 AC: 41 AN: 4818

European-Finnish (FIN) AF: 0.0252 AC: 267 AN: 10614

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0477 AC: 3244 AN: 67974

Other (OTH) AF: 0.0427 AC: 90 AN: 2110

Alfa AF: 0.0427 Hom.: 23

Bravo AF: 0.0410

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.010
DANN	Benign	0.35
PhyloP100		-4.2
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs28364018; hg19: chr8-67089870;