dbSNP rs2838859: POFUT2:c.*880G>A (chr21-45264602-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_133635.6(POFUT2):c.*880G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,918 control chromosomes in the GnomAD database, including 13,492 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 0.41 ( 13478 hom., cov: 31)

Exomes 𝑓: 0.34 ( 14 hom. )

Consequence

POFUT2
NM_133635.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.60

Publications

19 publications found

Variant links:

Genes affected

POFUT2 (HGNC:14683): (protein O-fucosyltransferase 2) Fucose is typically found as a terminal modification of branched chain glycoconjugates, but it also exists in direct O-linkage to serine or threonine residues within cystine knot motifs in epidermal growth factor (EGF; MIM 131530)-like repeats or thrombospondin (THBS; see MIM 188060) type-1 repeats. POFUT2 is an O-fucosyltransferase that use THBS type-1 repeats as substrates (Luo et al., 2006 [PubMed 16464857]).[supplied by OMIM, Mar 2008]

POFUT2 links:

LINC00334 (HGNC:16425): (long intergenic non-protein coding RNA 334)

LINC00334 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_133635.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
POFUT2	NM_133635.6	MANE Select	c.*880G>A	3_prime_UTR	Exon 9 of 9	NP_598368.2
POFUT2	NM_015227.6		c.*2849G>A	3_prime_UTR	Exon 8 of 8	NP_056042.1	Q9Y2G5-1
POFUT2	NR_004858.3		n.2400G>A	non_coding_transcript_exon	Exon 10 of 10

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
POFUT2	ENST00000349485.10	TSL:1 MANE Select	c.*880G>A	3_prime_UTR	Exon 9 of 9	ENSP00000339613.5	Q9Y2G5-3
POFUT2	ENST00000331343.11	TSL:1	c.*2849G>A	3_prime_UTR	Exon 8 of 8	ENSP00000329682.7	Q9Y2G5-1
POFUT2	ENST00000615172.4	TSL:1	c.*1233G>A	3_prime_UTR	Exon 6 of 6	ENSP00000482216.1	A0A0C4DGX7

Frequencies

GnomAD3 genomes

AF:

0.413

AC:

62627

AN:

151526

Hom.:

13459

Cov.:

show subpopulations

Gnomad AFR

AF:

0.526

Gnomad AMI

AF:

0.385

Gnomad AMR

AF:

0.333

Gnomad ASJ

AF:

0.370

Gnomad EAS

AF:

0.458

Gnomad SAS

AF:

0.540

Gnomad FIN

AF:

0.350

Gnomad MID

AF:

0.455

Gnomad NFE

AF:

0.363

Gnomad OTH

AF:

0.411

GnomAD4 exome

AF:

0.343

AC:

AN:

274

Hom.:

Cov.:

AF XY:

0.332

AC XY:

AN XY:

208

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.250

AC:

AN:

South Asian (SAS)

AF:

0.300

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

0.333

AC:

AN:

European-Non Finnish (NFE)

AF:

0.333

AC:

AN:

222

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.413

AC:

62695

AN:

151644

Hom.:

13478

Cov.:

AF XY:

0.417

AC XY:

30876

AN XY:

74104

show subpopulations

African (AFR)

AF:

0.527

AC:

21746

AN:

41294

American (AMR)

AF:

0.333

AC:

5069

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.370

AC:

1283

AN:

3468

East Asian (EAS)

AF:

0.459

AC:

2359

AN:

5144

South Asian (SAS)

AF:

0.539

AC:

2587

AN:

4800

European-Finnish (FIN)

AF:

0.350

AC:

3669

AN:

10496

Middle Eastern (MID)

AF:

0.459

AC:

134

AN:

292

European-Non Finnish (NFE)

AF:

0.363

AC:

24635

AN:

67892

Other (OTH)

AF:

0.409

AC:

863

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1852

3704

5557

7409

9261

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

608

1216

1824

2432

3040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.379

Hom.:

41524

Bravo

AF:

0.414

Asia WGS

AF:

0.487

AC:

1696

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

0.53

(source)

DANN

Benign

0.51

PhyloP100

-1.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over