Variant 17-63881309-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002059.5(GH2):c.171+50C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 1,612,074 control chromosomes in the GnomAD database, including 76,592 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 0.38 ( 14431 hom., cov: 32)

Exomes 𝑓: 0.28 ( 62161 hom. )

Consequence

GH2
NM_002059.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.212

Variant links:

Genes affected

GH2 (HGNC:4262): (growth hormone 2) The protein encoded by this gene is a member of the somatotropin/prolactin family of hormones which play an important role in growth control. The gene, along with four other related genes, is located at the growth hormone locus on chromosome 17 where they are interspersed in the same transcriptional orientation; an arrangement which is thought to have evolved by a series of gene duplications. The five genes share a remarkably high degree of sequence identity. Alternative splicing generates additional isoforms of each of the five growth hormones, leading to further diversity and potential for specialization. As in the case of its pituitary counterpart, growth hormone 1, the predominant isoform of this particular family member shows similar somatogenic activity, with reduced lactogenic activity. Mutations in this gene lead to placental growth hormone/lactogen deficiency. [provided by RefSeq, Jul 2008]

GH2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
GH2	NM_002059.5 linkuse as main transcript	c.171+50C>A	intron_variant	ENST00000423893.7
GH2	NM_022556.4 linkuse as main transcript	c.171+50C>A	intron_variant
GH2	NM_022557.4 linkuse as main transcript	c.171+50C>A	intron_variant
GH2	NM_022558.4 linkuse as main transcript	c.171+50C>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GH2	ENST00000423893.7 linkuse as main transcript	c.171+50C>A		intron_variant		1	NM_002059.5	P1	P01242-1

Frequencies

GnomAD3 genomes

AF:

0.379

AC:

57601

AN:

151794

Hom.:

14381

Cov.:

show subpopulations

Gnomad AFR

AF:

0.711

Gnomad AMI

AF:

0.270

Gnomad AMR

AF:

0.250

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.0555

Gnomad SAS

AF:

0.174

Gnomad FIN

AF:

0.203

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.282

Gnomad OTH

AF:

0.345

GnomAD3 exomes

AF:

0.265

AC:

66475

AN:

250732

Hom.:

11381

AF XY:

0.258

AC XY:

34996

AN XY:

135824

show subpopulations

Gnomad AFR exome

AF:

0.720

Gnomad AMR exome

AF:

0.220

Gnomad ASJ exome

AF:

0.275

Gnomad EAS exome

AF:

0.0464

Gnomad SAS exome

AF:

0.177

Gnomad FIN exome

AF:

0.215

Gnomad NFE exome

AF:

0.284

Gnomad OTH exome

AF:

0.255

GnomAD4 exome

AF:

0.275

AC:

401677

AN:

1460162

Hom.:

62161

Cov.:

AF XY:

0.272

AC XY:

197361

AN XY:

726542

show subpopulations

Gnomad4 AFR exome

AF:

0.726

Gnomad4 AMR exome

AF:

0.225

Gnomad4 ASJ exome

AF:

0.276

Gnomad4 EAS exome

AF:

0.0499

Gnomad4 SAS exome

AF:

0.181

Gnomad4 FIN exome

AF:

0.221

Gnomad4 NFE exome

AF:

0.281

Gnomad4 OTH exome

AF:

0.274

GnomAD4 genome

AF:

0.380

AC:

57693

AN:

151912

Hom.:

14431

Cov.:

AF XY:

0.370

AC XY:

27438

AN XY:

74246

show subpopulations

Gnomad4 AFR

AF:

0.712

Gnomad4 AMR

AF:

0.249

Gnomad4 ASJ

AF:

0.276

Gnomad4 EAS

AF:

0.0556

Gnomad4 SAS

AF:

0.172

Gnomad4 FIN

AF:

0.203

Gnomad4 NFE

AF:

0.282

Gnomad4 OTH

AF:

0.341

Alfa

AF:

0.324

Hom.:

1787

Bravo

AF:

0.398

Asia WGS

AF:

0.161

AC:

564

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.070

DANN

Benign

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over