Variant 7-30977488-G-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_000823.4(GHRHR):c.1146+166G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,070 control chromosomes in the GnomAD database, including 9,824 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.34 ( 9824 hom., cov: 32)

Consequence

GHRHR
NM_000823.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.239

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BP6

Variant 7-30977488-G-C is Benign according to our data. Variant chr7-30977488-G-C is described in ClinVar as [Benign]. Clinvar id is 1259484.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GHRHR	NM_000823.4 linkuse as main transcript	c.1146+166G>C		intron_variant		ENST00000326139.7	NP_000814.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GHRHR	ENST00000326139.7 linkuse as main transcript	c.1146+166G>C		intron_variant		1	NM_000823.4	ENSP00000320180	P1

Frequencies

GnomAD3 genomes

AF:

0.341

AC:

51833

AN:

151950

Hom.:

9786

Cov.:

show subpopulations

Gnomad AFR

AF:

0.496

Gnomad AMI

AF:

0.328

Gnomad AMR

AF:

0.247

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.0350

Gnomad SAS

AF:

0.297

Gnomad FIN

AF:

0.303

Gnomad MID

AF:

0.268

Gnomad NFE

AF:

0.309

Gnomad OTH

AF:

0.296

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

GnomAD4 genome

AF:

0.341

AC:

51926

AN:

152070

Hom.:

9824

Cov.:

AF XY:

0.337

AC XY:

25088

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.497

Gnomad4 AMR

AF:

0.247

Gnomad4 ASJ

AF:

0.212

Gnomad4 EAS

AF:

0.0349

Gnomad4 SAS

AF:

0.300

Gnomad4 FIN

AF:

0.303

Gnomad4 NFE

AF:

0.309

Gnomad4 OTH

AF:

0.298

Alfa

AF:

0.172

Hom.:

322

Bravo

AF:

0.339

Asia WGS

AF:

0.214

AC:

746

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

-0.47

CADD

Benign

DANN

Benign

0.77

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

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