7-30963834-C-T

Position:

• chr7-30963834-C-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.285-5000C>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 0.348 in 152,180 control chromosomes in the GnomAD database, including 10,200 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.35 (10200 hom., cov: 34)
• Consequence: GHRHR ENST00000466427.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.125

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=-0.84).
• BP6: Variant 7-30963834-C-T is Benign according to our data. Variant chr7-30963834-C-T is described in ClinVar as [Benign]. Clinvar id is 1221154.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GHRHR	ENST00000466427.1	n.285-5000C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52945 AN: 152062 Hom.: 10184 Cov.: 34

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.0793

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.348 AC: 52993 AN: 152180 Hom.: 10200 Cov.: 34 AF XY: 0.342 AC XY: 25419 AN XY: 74396

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.0791

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.333

Alfa AF: 0.319 Hom.: 3950

Bravo AF: 0.353

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2302020; hg19: chr7-31003449; COSMIC: COSV58198675;