rs13088281

Positions:

• chr3-53113560-C-A

Variant summary

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

The NM_052859.4(RFT1):​c.697-1652G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0777 in 152,254 control chromosomes in the GnomAD database, including 565 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 0.078 (565 hom., cov: 33)
• Consequence: RFT1 NM_052859.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

RFT1 (HGNC:30220): (RFT1 homolog) This gene encodes an enzyme which catalyzes the translocation of the Man(5)GlcNAc (2)-PP-Dol intermediate from the cytoplasmic to the luminal side of the endoplasmic reticulum membrane in the pathway for the N-glycosylation of proteins. Mutations in this gene are associated with congenital disorder of glycosylation type In.[provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RFT1	NM_052859.4	c.697-1652G>T		intron_variant		ENST00000296292.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RFT1	ENST00000296292.8	c.697-1652G>T		intron_variant		1	NM_052859.4	P1
RFT1	ENST00000394738.7	c.580-1652G>T		intron_variant		5
RFT1	ENST00000467048.1	c.559-1652G>T		intron_variant		3
RFT1	ENST00000471158.1	n.139-1652G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0777 AC: 11821 AN: 152136 Hom.: 561 Cov.: 33

Gnomad AFR AF: 0.0229

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0902

Gnomad FIN AF: 0.0834

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.0777 AC: 11829 AN: 152254 Hom.: 565 Cov.: 33 AF XY: 0.0770 AC XY: 5730 AN XY: 74426

Gnomad4 AFR AF: 0.0229

Gnomad4 AMR AF: 0.0952

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.0909

Gnomad4 FIN AF: 0.0834

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0972

Alfa AF: 0.0971 Hom.: 714

Bravo AF: 0.0767

Asia WGS AF: 0.0910 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.4
DANN	Benign	0.76

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: rs13088281; hg19: chr3-53147576;