chr8-33397242-C-T

Variant names:

• chr8-33397242-C-T
• rs10503944
• NM_032664.3:c.377-7444G>A

Variant summary

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

The NM_032664.3(POFUT3):​c.377-7444G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,044 control chromosomes in the GnomAD database, including 3,510 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 0.20 (3510 hom., cov: 32)
• Consequence: POFUT3 NM_032664.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032664.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POFUT3	NM_032664.3	MANE Select	c.377-7444G>A		intron	N/A	NP_116053.3	Q6P4F1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FUT10	ENST00000327671.10	TSL:1 MANE Select	c.377-7444G>A		intron	N/A	ENSP00000332757.5	Q6P4F1-1
	FUT10	ENST00000518672.5	TSL:1	c.293-7444G>A		intron	N/A	ENSP00000430428.1	Q6P4F1-6
	FUT10	ENST00000520767.5	TSL:1	n.721-7444G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29914 AN: 151926 Hom.: 3512 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.197 AC: 29910 AN: 152044 Hom.: 3510 Cov.: 32 AF XY: 0.202 AC XY: 15023 AN XY: 74312

African (AFR) AF: 0.125 AC: 5184 AN: 41460

American (AMR) AF: 0.188 AC: 2874 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3470

East Asian (EAS) AF: 0.465 AC: 2403 AN: 5168

South Asian (SAS) AF: 0.459 AC: 2211 AN: 4822

European-Finnish (FIN) AF: 0.197 AC: 2074 AN: 10548

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13467 AN: 67994

Other (OTH) AF: 0.196 AC: 413 AN: 2106

Alfa AF: 0.182 Hom.: 354

Bravo AF: 0.191

Asia WGS AF: 0.423 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.9
DANN	Benign	0.56
PhyloP100		0.22
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: rs10503944; hg19: chr8-33254760;