chr11-94544295-A-C
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_002033.4(FUT4):āc.162A>Cā(p.Pro54=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00249 in 1,563,300 control chromosomes in the GnomAD database, including 79 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.013 ( 47 hom., cov: 33)
Exomes š: 0.0013 ( 32 hom. )
Consequence
FUT4
NM_002033.4 synonymous
NM_002033.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.45
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 11-94544295-A-C is Benign according to our data. Variant chr11-94544295-A-C is described in ClinVar as [Benign]. Clinvar id is 776650.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-5.45 with no splicing effect.
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0505 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FUT4 | NM_002033.4 | c.162A>C | p.Pro54= | synonymous_variant | 1/1 | ENST00000358752.4 | NP_002024.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FUT4 | ENST00000358752.4 | c.162A>C | p.Pro54= | synonymous_variant | 1/1 | NM_002033.4 | ENSP00000351602 | P1 | ||
PIWIL4 | ENST00000543336.5 | c.-121+306A>C | intron_variant, NMD_transcript_variant | 2 | ENSP00000444575 |
Frequencies
GnomAD3 genomes AF: 0.0132 AC: 2010AN: 152110Hom.: 46 Cov.: 33
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GnomAD3 exomes AF: 0.00183 AC: 321AN: 175146Hom.: 4 AF XY: 0.00136 AC XY: 135AN XY: 99052
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GnomAD4 exome AF: 0.00133 AC: 1878AN: 1411082Hom.: 32 Cov.: 31 AF XY: 0.00118 AC XY: 828AN XY: 700770
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GnomAD4 genome AF: 0.0133 AC: 2021AN: 152218Hom.: 47 Cov.: 33 AF XY: 0.0128 AC XY: 955AN XY: 74420
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 15, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at