8-27571711-C-T

Variant names:

• chr8-27571711-C-T
• rs1316801
• ENST00000454030.1:n.198-5900C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000454030.1(GULOP):​n.198-5900C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 152,018 control chromosomes in the GnomAD database, including 23,046 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 (23046 hom., cov: 31)
• Consequence: GULOP ENST00000454030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GULOP	ENST00000454030.1	n.198-5900C>T		intron_variant	Intron 2 of 5	6

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79550 AN: 151900 Hom.: 23019 Cov.: 31

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.524 AC: 79622 AN: 152018 Hom.: 23046 Cov.: 31 AF XY: 0.522 AC XY: 38750 AN XY: 74290

African (AFR) AF: 0.783 AC: 32458 AN: 41478

American (AMR) AF: 0.416 AC: 6361 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1761 AN: 3472

East Asian (EAS) AF: 0.617 AC: 3172 AN: 5142

South Asian (SAS) AF: 0.571 AC: 2750 AN: 4812

European-Finnish (FIN) AF: 0.360 AC: 3801 AN: 10568

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27639 AN: 67934

Other (OTH) AF: 0.518 AC: 1096 AN: 2114

Alfa AF: 0.448 Hom.: 54150

Bravo AF: 0.539

Asia WGS AF: 0.573 AC: 1996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.53
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs1316801; hg19: chr8-27429228;