rs2741352

Variant names:

• chr8-27560442-T-C
• rs2741352
• ENST00000454030.1:n.101+68T>C

Variant summary

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

The ENST00000454030.1(GULOP):​n.101+68T>C 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 152,216 control chromosomes in the GnomAD database, including 22,211 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 (22191 hom., cov: 33)
  • Exomes 𝑓: 0.55 (20 hom.)
• Consequence: GULOP ENST00000454030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.65
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.61 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.101+68T>C		intron_variant	Intron 1 of 5	6

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79633 AN: 151982 Hom.: 22175 Cov.: 33

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.525

GnomAD4 exome AF: 0.552 AC: 64 AN: 116 Hom.: 20 AF XY: 0.544 AC XY: 49 AN XY: 90

African (AFR) AC: 0 AN: 0

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.250 AC: 1 AN: 4

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.523 AC: 45 AN: 86

Other (OTH) AF: 0.700 AC: 14 AN: 20

GnomAD4 genome AF: 0.524 AC: 79690 AN: 152100 Hom.: 22191 Cov.: 33 AF XY: 0.525 AC XY: 39025 AN XY: 74378

African (AFR) AF: 0.348 AC: 14428 AN: 41478

American (AMR) AF: 0.621 AC: 9494 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1896 AN: 3466

East Asian (EAS) AF: 0.254 AC: 1308 AN: 5158

South Asian (SAS) AF: 0.483 AC: 2329 AN: 4820

European-Finnish (FIN) AF: 0.626 AC: 6632 AN: 10590

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41624 AN: 67976

Other (OTH) AF: 0.531 AC: 1121 AN: 2112

Alfa AF: 0.575 Hom.: 16915

Bravo AF: 0.515

Asia WGS AF: 0.419 AC: 1457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.072
DANN	Benign	0.57
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs2741352; hg19: chr8-27417959;