14-54881109-A-G

Position:

• chr14-54881109-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000161.3(GCH1):​c.344-15673T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,242 control chromosomes in the GnomAD database, including 21,665 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 0.52 (21665 hom., cov: 28)
• Consequence: GCH1 NM_000161.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

Genes affected

GCH1 (HGNC:4193): (GTP cyclohydrolase 1) This gene encodes a member of the GTP cyclohydrolase family. The encoded protein is the first and rate-limiting enzyme in tetrahydrobiopterin (BH4) biosynthesis, catalyzing the conversion of GTP into 7,8-dihydroneopterin triphosphate. BH4 is an essential cofactor required by aromatic amino acid hydroxylases as well as nitric oxide synthases. Mutations in this gene are associated with malignant hyperphenylalaninemia and dopa-responsive dystonia. Several alternatively spliced transcript variants encoding different isoforms have been described; however, not all variants give rise to a functional enzyme. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GCH1	NM_000161.3	c.344-15673T>C		intron_variant		ENST00000491895.7	NP_000152.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GCH1	ENST00000491895.7	c.344-15673T>C		intron_variant		1	NM_000161.3	ENSP00000419045	P1

Frequencies

GnomAD3 genomes AF: 0.521 AC: 78729 AN: 151128 Hom.: 21620 Cov.: 28

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.521 AC: 78841 AN: 151242 Hom.: 21665 Cov.: 28 AF XY: 0.526 AC XY: 38800 AN XY: 73820

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.460

Alfa AF: 0.491 Hom.: 2367

Bravo AF: 0.518

Asia WGS AF: 0.484 AC: 1681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.37

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: rs7155501; hg19: chr14-55347827;