8-33426489-T-C

Variant names:

• chr8-33426489-T-C
• rs2459516
• NM_032664.3:c.376+26727A>G

Variant summary

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

The NM_032664.3(POFUT3):​c.376+26727A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 152,086 control chromosomes in the GnomAD database, including 37,633 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 0.69 (37633 hom., cov: 32)
• Consequence: POFUT3 NM_032664.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967
• Publications: 2 publications found

Genes affected

POFUT3 (HGNC:19234): (fucosyltransferase 10) Predicted to enable alpha-(1->3)-fucosyltransferase activity. Predicted to be involved in fucosylation. Predicted to act upstream of or within cerebral cortex radially oriented cell migration and neuronal stem cell population maintenance. Located in Golgi apparatus; endoplasmic reticulum; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POFUT3	NM_032664.3	c.376+26727A>G		intron_variant	Intron 3 of 4	ENST00000327671.10	NP_116053.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FUT10	ENST00000327671.10	c.376+26727A>G		intron_variant	Intron 3 of 4	1	NM_032664.3	ENSP00000332757.5

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105402 AN: 151968 Hom.: 37575 Cov.: 32

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.694 AC: 105519 AN: 152086 Hom.: 37633 Cov.: 32 AF XY: 0.692 AC XY: 51399 AN XY: 74318

African (AFR) AF: 0.858 AC: 35601 AN: 41498

American (AMR) AF: 0.581 AC: 8863 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2127 AN: 3472

East Asian (EAS) AF: 0.581 AC: 3003 AN: 5172

South Asian (SAS) AF: 0.508 AC: 2446 AN: 4816

European-Finnish (FIN) AF: 0.662 AC: 6994 AN: 10562

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44236 AN: 67988

Other (OTH) AF: 0.671 AC: 1416 AN: 2110

Alfa AF: 0.669 Hom.: 8249

Bravo AF: 0.696

Asia WGS AF: 0.545 AC: 1898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.27
DANN	Benign	0.70
PhyloP100		-0.97
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2459516; hg19: chr8-33284007;