8-33397242-C-T

Position:

• chr8-33397242-C-T

Variant summary

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

The NM_032664.3(FUT10):​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: FUT10 NM_032664.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

Genes affected

FUT10 (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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FUT10	NM_032664.3	c.377-7444G>A		intron_variant		ENST00000327671.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FUT10	ENST00000327671.10	c.377-7444G>A		intron_variant		1	NM_032664.3	P1

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

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.196

Alfa AF: 0.183 Hom.: 350

Bravo AF: 0.191

Asia WGS AF: 0.423 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.9
DANN	Benign	0.56

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: rs10503944; hg19: chr8-33254760;