chr7-30963808-C-T

Variant names:

• chr7-30963808-C-T
• rs2302019
• ENST00000466427.1:n.285-5026C>T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000466427.1(GHRHR):​n.285-5026C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,104 control chromosomes in the GnomAD database, including 26,039 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.55 (26039 hom., cov: 33)
• Consequence: GHRHR ENST00000466427.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.834

Genes affected

GHRHR (HGNC:4266): (growth hormone releasing hormone receptor) This gene encodes a receptor for growth hormone-releasing hormone. Binding of this hormone to the receptor leads to synthesis and release of growth hormone. Mutations in this gene have been associated with isolated growth hormone deficiency (IGHD), also known as Dwarfism of Sindh, a disorder characterized by short stature. [provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 7-30963808-C-T is Benign according to our data. Variant chr7-30963808-C-T is described in ClinVar as [Benign]. Clinvar id is 1258935.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GHRHR	NM_000823.4	c.-261C>T		upstream_gene_variant		ENST00000326139.7	NP_000814.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GHRHR	ENST00000466427.1	n.285-5026C>T		intron_variant	Intron 1 of 1	5
GHRHR	ENST00000326139.7	c.-261C>T		upstream_gene_variant		1	NM_000823.4	ENSP00000320180.2

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82797 AN: 151986 Hom.: 25982 Cov.: 33

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.545 AC: 82904 AN: 152104 Hom.: 26039 Cov.: 33 AF XY: 0.540 AC XY: 40148 AN XY: 74332

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.548

Alfa AF: 0.446 Hom.: 32829

Bravo AF: 0.561

Asia WGS AF: 0.519 AC: 1805 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 16606630) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.72
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2302019; hg19: chr7-31003423;