rs2292767

chr10-118590524-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_004248.3(PRLHR):c.*3608G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,124 control chromosomes in the GnomAD database, including 7,183 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 0.28 (7183 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: PRLHR NM_004248.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

Genes affected

PRLHR (HGNC:4464): (prolactin releasing hormone receptor) Predicted to enable neuropeptide receptor activity. Predicted to be involved in female pregnancy. Predicted to act upstream of or within G protein-coupled receptor signaling pathway; feeding behavior; and hormone metabolic process. Located in cilium. Implicated in hypertension. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRLHR	NM_004248.3	c.*3608G>A		3_prime_UTR_variant	2/2	ENST00000239032.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRLHR	ENST00000239032.4	c.*3608G>A		3_prime_UTR_variant	2/2	1	NM_004248.3	P1

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42179 AN: 152004 Hom.: 7187 Cov.: 32

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.260

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.277 AC: 42165 AN: 152122 Hom.: 7183 Cov.: 32 AF XY: 0.276 AC XY: 20525 AN XY: 74350

Gnomad4 AFR AF: 0.0899

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.257

Alfa AF: 0.354 Hom.: 13801

Bravo AF: 0.257

Asia WGS AF: 0.226 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
Cadd	Benign	16
Dann	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs2292767; hg19: chr10-120350036;