Variant chr20-32207926-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_015352.2(POFUT1):c.-16G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00407 in 1,576,262 control chromosomes in the GnomAD database, including 234 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0072 ( 34 hom., cov: 32)

Exomes 𝑓: 0.0037 ( 200 hom. )

Consequence

POFUT1
NM_015352.2 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.319

Variant links:

Genes affected

POFUT1 (HGNC:14988): (protein O-fucosyltransferase 1) This gene encodes a member of the glycosyltransferase O-Fuc family. This enzyme adds O-fucose through an O-glycosidic linkage to conserved serine or threonine residues in the epidermal growth factor-like repeats of a number of cell surface and secreted proteins. O-fucose glycans are involved in ligand-induced receptor signaling. Alternative splicing of this gene results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

POFUT1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 20-32207926-G-C is Benign according to our data. Variant chr20-32207926-G-C is described in ClinVar as [Benign]. Clinvar id is 1179440.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
POFUT1	NM_015352.2 linkuse as main transcript	c.-16G>C	5_prime_UTR_variant	1/7	ENST00000375749.8	NP_056167.1
POFUT1	NM_172236.2 linkuse as main transcript	c.-16G>C	5_prime_UTR_variant	1/5		NP_758436.1
POFUT1	XM_047440079.1 linkuse as main transcript	c.-218G>C	5_prime_UTR_variant	1/6		XP_047296035.1
POFUT1	XR_007067447.1 linkuse as main transcript	n.47G>C	non_coding_transcript_exon_variant	1/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POFUT1	ENST00000375749.8 linkuse as main transcript	c.-16G>C		5_prime_UTR_variant	1/7	1	NM_015352.2	ENSP00000364902	P1	Q9H488-1

Frequencies

GnomAD3 genomes

AF:

0.00709

AC:

1077

AN:

151880

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00234

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0528

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.0210

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000486

Gnomad OTH

AF:

0.00959

GnomAD3 exomes

AF:

0.0176

AC:

3407

AN:

193926

Hom.:

158

AF XY:

0.0130

AC XY:

1411

AN XY:

108446

show subpopulations

Gnomad AFR exome

AF:

0.00199

Gnomad AMR exome

AF:

0.0946

Gnomad ASJ exome

AF:

0.00312

Gnomad EAS exome

AF:

0.0197

Gnomad SAS exome

AF:

0.000550

Gnomad FIN exome

AF:

0.000544

Gnomad NFE exome

AF:

0.000589

Gnomad OTH exome

AF:

0.0128

GnomAD4 exome

AF:

0.00374

AC:

5329

AN:

1424268

Hom.:

200

Cov.:

AF XY:

0.00325

AC XY:

2302

AN XY:

707530

show subpopulations

Gnomad4 AFR exome

AF:

0.00133

Gnomad4 AMR exome

AF:

0.0886

Gnomad4 ASJ exome

AF:

0.00312

Gnomad4 EAS exome

AF:

0.0224

Gnomad4 SAS exome

AF:

0.000576

Gnomad4 FIN exome

AF:

0.000956

Gnomad4 NFE exome

AF:

0.000242

Gnomad4 OTH exome

AF:

0.00413

GnomAD4 genome

AF:

0.00716

AC:

1088

AN:

151994

Hom.:

Cov.:

AF XY:

0.00769

AC XY:

571

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.00234

Gnomad4 AMR

AF:

0.0535

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.0210

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000486

Gnomad4 OTH

AF:

0.00949

Alfa

AF:

0.00337

Hom.:

Bravo

AF:

0.0119

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 05, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.99

DANN

Benign

0.37

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over