Variant chr7-30963834-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000466427.1(GHRHR):n.285-5000C>T variant causes a intron 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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.125

Variant links:

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]

GHRHR links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GHRHR	ENST00000466427.1 linkuse as main transcript	n.285-5000C>T		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.348

AC:

52945

AN:

152062

Hom.:

10184

Cov.:

show subpopulations

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.:

AF XY:

0.342

AC XY:

25419

AN XY:

74396

show subpopulations

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

LINK: link

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over