rs7147624

Positions:

• chr14-65398907-T-G

Variant summary

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

The XM_047431179.1(FUT8):​c.-390+22033T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,190 control chromosomes in the GnomAD database, including 51,682 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 0.82 (51682 hom., cov: 32)
• Consequence: FUT8 XM_047431179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

Genes affected

FUT8 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FUT8	XM_047431179.1	c.-390+22033T>G		intron_variant			XP_047287135.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124939 AN: 152072 Hom.: 51643 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.822 AC: 125037 AN: 152190 Hom.: 51682 Cov.: 32 AF XY: 0.826 AC XY: 61498 AN XY: 74422

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.824

Alfa AF: 0.838 Hom.: 29042

Bravo AF: 0.813

Asia WGS AF: 0.934 AC: 3246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7147624; hg19: chr14-65865625;