rs17057419

Variant names:

• chr8-27579871-A-G
• rs17057419

Variant summary

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

The variant allele was found at a frequency of 0.222 in 152,060 control chromosomes in the GnomAD database, including 4,527 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 0.22 (4527 hom., cov: 32)
• Consequence: GULOP intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 5 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454030.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GULOP	ENST00000454030.1	TSL:6	n.304+2154A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33703 AN: 151940 Hom.: 4529 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.0670

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.222 AC: 33735 AN: 152060 Hom.: 4527 Cov.: 32 AF XY: 0.221 AC XY: 16448 AN XY: 74306

African (AFR) AF: 0.344 AC: 14265 AN: 41468

American (AMR) AF: 0.214 AC: 3272 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 821 AN: 3472

East Asian (EAS) AF: 0.430 AC: 2216 AN: 5158

South Asian (SAS) AF: 0.344 AC: 1651 AN: 4800

European-Finnish (FIN) AF: 0.0670 AC: 710 AN: 10604

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10122 AN: 67962

Other (OTH) AF: 0.210 AC: 443 AN: 2112

Alfa AF: 0.173 Hom.: 5046

Bravo AF: 0.238

Asia WGS AF: 0.374 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.30
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs17057419; hg19: chr8-27437388;