rs1402919569

Variant names:

• chr11-94544408-G-T
• rs1402919569
• NM_002033.4:c.275G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-94544408-G-T
• chr11-94544408-G-A
• chr11-94544408-G-C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_002033.4(FUT4):​c.275G>T​(p.Arg92Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,376,894 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.000012 (0 hom.)
• Consequence: FUT4 NM_002033.4 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.106
• Publications: 0 publications found

Genes affected

FUT4 (HGNC:4015): (fucosyltransferase 4) The product of this gene transfers fucose to N-acetyllactosamine polysaccharides to generate fucosylated carbohydrate structures. It catalyzes the synthesis of the non-sialylated antigen, Lewis x (CD15). [provided by RefSeq, Jan 2009]

PIWIL4 (HGNC:18444): (piwi like RNA-mediated gene silencing 4) PIWIL4 belongs to the Argonaute family of proteins, which function in development and maintenance of germline stem cells (Sasaki et al., 2003 [PubMed 12906857]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.034614354).
• BP6: Variant 11-94544408-G-T is Benign according to our data. Variant chr11-94544408-G-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3097496.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002033.4. 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
	FUT4	NM_002033.4	MANE Select	c.275G>T	p.Arg92Leu	missense	Exon 1 of 1	NP_002024.1	P22083-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FUT4	ENST00000358752.4	TSL:6 MANE Select	c.275G>T	p.Arg92Leu	missense	Exon 1 of 1	ENSP00000351602.2	P22083-1
	PIWIL4	ENST00000543336.5	TSL:2	n.-121+419G>T		intron	N/A	ENSP00000444575.1	Q7Z3Z4-3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD2 exomes AF: 0.0000163 AC: 2 AN: 123044 AF XY: 0.0000290

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000212

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000116 AC: 16 AN: 1376894 Hom.: 0 Cov.: 31 AF XY: 0.0000132 AC XY: 9 AN XY: 680942

African (AFR) AF: 0.00 AC: 0 AN: 28974

American (AMR) AF: 0.00 AC: 0 AN: 36518

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24616

East Asian (EAS) AF: 0.00 AC: 0 AN: 33888

South Asian (SAS) AF: 0.0000126 AC: 1 AN: 79094

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33990

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4376

European-Non Finnish (NFE) AF: 0.0000139 AC: 15 AN: 1077990

Other (OTH) AF: 0.00 AC: 0 AN: 57448

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	16
DANN	Benign	0.62
DEOGEN2	Benign	0.11	T
Eigen	Benign	-2.2
Eigen_PC	Benign	-2.3
FATHMM_MKL	Benign	0.0065	N
LIST_S2	Benign	0.38	T
M_CAP	Benign	0.066	D
MetaRNN	Benign	0.035	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
PhyloP100		-0.11
PrimateAI	Uncertain	0.73	T
PROVEAN	Benign	-0.30	N
REVEL	Benign	0.0030
Sift	Benign	1.0	T
Sift4G	Pathogenic	0.0	D
Polyphen		0.0	B
Vest4		0.070
MutPred		0.19		Gain of helix (P = 0.0325)
MVP		0.12
MPC		0.97
ClinPred		0.040	T
GERP RS		-5.8
PromoterAI		-0.018	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.052
gMVP		0.31
Mutation Taster		=92/8	polymorphism

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: rs1402919569; hg19: chr11-94277574;