chr19-5867166-G-A

Variant names:

• chr19-5867166-G-A
• rs778970
• NM_002034.2:c.560C>T

Variant summary

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

The NM_002034.2(FUT5):​c.560C>T​(p.Pro187Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 1,610,964 control chromosomes in the GnomAD database, including 170,867 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.42 (14191 hom., cov: 30)
  • Exomes 𝑓: 0.46 (156676 hom.)
• Consequence: FUT5 NM_002034.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.475
• Publications: 23 publications found

Genes affected

FUT5 (HGNC:4016): (fucosyltransferase 5) Enables 3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity and 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase activity. Involved in ceramide metabolic process and oligosaccharide metabolic process. Predicted to be located in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000267740 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=2.8676883E-5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002034.2. 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
	FUT5	NM_002034.2	MANE Select	c.560C>T	p.Pro187Leu	missense	Exon 2 of 2	NP_002025.2	Q11128

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FUT5	ENST00000588525.1	TSL:1 MANE Select	c.560C>T	p.Pro187Leu	missense	Exon 2 of 2	ENSP00000466880.1	Q11128
	FUT5	ENST00000252675.6	TSL:6	c.560C>T	p.Pro187Leu	missense	Exon 1 of 1	ENSP00000252675.5	Q11128
	ENSG00000267740	ENST00000592091.5	TSL:2	n.*678C>T		non_coding_transcript_exon	Exon 5 of 5	ENSP00000465499.1	K7EK78

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64248 AN: 151368 Hom.: 14179 Cov.: 30

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.411

GnomAD2 exomes AF: 0.473 AC: 115488 AN: 244406 AF XY: 0.466

Gnomad AFR exome AF: 0.304

Gnomad AMR exome AF: 0.630

Gnomad ASJ exome AF: 0.447

Gnomad EAS exome AF: 0.577

Gnomad FIN exome AF: 0.420

Gnomad NFE exome AF: 0.457

Gnomad OTH exome AF: 0.477

GnomAD4 exome AF: 0.462 AC: 674354 AN: 1459480 Hom.: 156676 Cov.: 84 AF XY: 0.460 AC XY: 333922 AN XY: 726054

African (AFR) AF: 0.312 AC: 10432 AN: 33448

American (AMR) AF: 0.622 AC: 27743 AN: 44636

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 11780 AN: 26110

East Asian (EAS) AF: 0.622 AC: 24662 AN: 39618

South Asian (SAS) AF: 0.419 AC: 36097 AN: 86230

European-Finnish (FIN) AF: 0.425 AC: 22166 AN: 52186

Middle Eastern (MID) AF: 0.449 AC: 2577 AN: 5738

European-Non Finnish (NFE) AF: 0.460 AC: 511436 AN: 1111200

Other (OTH) AF: 0.455 AC: 27461 AN: 60314

GnomAD4 genome AF: 0.424 AC: 64293 AN: 151484 Hom.: 14191 Cov.: 30 AF XY: 0.427 AC XY: 31590 AN XY: 73950

African (AFR) AF: 0.308 AC: 12736 AN: 41350

American (AMR) AF: 0.545 AC: 8297 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1548 AN: 3464

East Asian (EAS) AF: 0.592 AC: 2970 AN: 5020

South Asian (SAS) AF: 0.414 AC: 1980 AN: 4786

European-Finnish (FIN) AF: 0.413 AC: 4352 AN: 10542

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.458 AC: 31045 AN: 67792

Other (OTH) AF: 0.412 AC: 868 AN: 2106

Alfa AF: 0.440 Hom.: 6448

Bravo AF: 0.434

ExAC AF: 0.455 AC: 54709

EpiCase AF: 0.460

EpiControl AF: 0.454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.66	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	11
DANN	Uncertain	0.99
Eigen	Benign	-0.21
Eigen_PC	Benign	-0.37
FATHMM_MKL	Benign	0.47	N
LIST_S2	Benign	0.77	T
MetaRNN	Benign	0.000029	T
MetaSVM	Benign	-0.94	T
PhyloP100		0.47
PrimateAI	Benign	0.30	T
PROVEAN	Pathogenic	-4.9	D
REVEL	Benign	0.077
Sift	Benign	0.31	T
Sift4G	Benign	0.092	T
Vest4		0.092
MPC		0.75
ClinPred		0.056	T
GERP RS		1.3
gMVP		0.34
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: rs778970; hg19: chr19-5867177; COSMIC: COSV53134845; COSMIC: COSV53134845;