chr14-54888313-C-T

Position:

• chr14-54888313-C-T

Variant summary

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

The NM_000161.3(GCH1):​c.343+14008G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,040 control chromosomes in the GnomAD database, including 2,494 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 0.15 (2494 hom., cov: 31)
• Consequence: GCH1 NM_000161.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GCH1	NM_000161.3	c.343+14008G>A		intron_variant		ENST00000491895.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GCH1	ENST00000491895.7	c.343+14008G>A		intron_variant		1	NM_000161.3	P1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23430 AN: 151922 Hom.: 2498 Cov.: 31

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0502

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.154 AC: 23424 AN: 152040 Hom.: 2494 Cov.: 31 AF XY: 0.147 AC XY: 10903 AN XY: 74310

Gnomad4 AFR AF: 0.0426

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0507

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.186

Alfa AF: 0.131 Hom.: 349

Bravo AF: 0.156

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.44

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: rs998259; hg19: chr14-55355031;