8-27583362-G-A

Position:

• chr8-27583362-G-A

Variant summary

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

The ENST00000454030.1(GULOP):​n.305-2598G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,238 control chromosomes in the GnomAD database, including 921 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 0.11 (921 hom., cov: 33)
• Consequence: GULOP ENST00000454030.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.915

Genes affected

GULOP (HGNC:4695): (gulonolactone (L-) oxidase, pseudogene) This gene is nonfunctional in humans and other primates. In most mammalian species the corresponding gene encodes L-gulono-gamma-lactone oxidase which catalyzes the last step of ascorbic acid biosynthesis. The human gene is a remnant that lacks five of twelve exons found in functional rodent genes. The loss of enzyme activity results in hypoascorbemia or the inability to synthesize vitamin C. [provided by RefSeq, Nov 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GULOP	ENST00000454030.1	n.305-2598G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16172 AN: 152120 Hom.: 926 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0480

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.106 AC: 16192 AN: 152238 Hom.: 921 Cov.: 33 AF XY: 0.106 AC XY: 7925 AN XY: 74442

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0480

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.113

Alfa AF: 0.118 Hom.: 2122

Bravo AF: 0.114

Asia WGS AF: 0.196 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.91
DANN	Benign	0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10216623; hg19: chr8-27440879;