8-25419625-G-GT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_001083111.2(GNRH1):c.238-166_238-165insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00575 in 142,034 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.0058 (4 hom., cov: 31)
• Consequence: GNRH1 NM_001083111.2 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.117

Genes affected

GNRH1 (HGNC:4419): (gonadotropin releasing hormone 1) This gene encodes a preproprotein that is proteolytically processed to generate a peptide that is a member of the gonadotropin-releasing hormone (GnRH) family of peptides. Alternative splicing results in multiple transcript variants, at least one of which is secreted and then cleaved to generate gonadoliberin-1 and GnRH-associated peptide 1. Gonadoliberin-1 stimulates the release of luteinizing and follicle stimulating hormones, which are important for reproduction. Mutations in this gene are associated with hypogonadotropic hypogonadism. [provided by RefSeq, Nov 2015]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 8-25419625-G-GT is Benign according to our data. Variant chr8-25419625-G-GT is described in ClinVar as [Likely_benign]. Clinvar id is 1204009.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00575 (817/142034) while in subpopulation SAS AF= 0.0295 (132/4478). AF 95% confidence interval is 0.0254. There are 4 homozygotes in gnomad4. There are 498 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 4 AR,Digenic gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNRH1	NM_001083111.2	c.238-166_238-165insA		intron_variant		ENST00000421054.7
GNRH1	NM_000825.3	c.250-166_250-165insA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNRH1	ENST00000421054.7	c.238-166_238-165insA		intron_variant		1	NM_001083111.2	P1
GNRH1	ENST00000276414.4	c.238-166_238-165insA		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.00577 AC: 820 AN: 142026 Hom.: 4 Cov.: 31

Gnomad AFR AF: 0.00307

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00666

Gnomad ASJ AF: 0.000905

Gnomad EAS AF: 0.0182

Gnomad SAS AF: 0.0302

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00338

Gnomad OTH AF: 0.00414

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

GnomAD4 genome AF: 0.00575 AC: 817 AN: 142034 Hom.: 4 Cov.: 31 AF XY: 0.00722 AC XY: 498 AN XY: 68958

Gnomad4 AFR AF: 0.00309

Gnomad4 AMR AF: 0.00666

Gnomad4 ASJ AF: 0.000905

Gnomad4 EAS AF: 0.0183

Gnomad4 SAS AF: 0.0295

Gnomad4 FIN AF: 0.0179

Gnomad4 NFE AF: 0.00338

Gnomad4 OTH AF: 0.00412

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 10, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs371851426; hg19: chr8-25277141;