19-35742670-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_144987.4(U2AF1L4):c.537G>C(p.Trp179Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144987.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
U2AF1L4 | ENST00000378975 | c.*49G>C | 3_prime_UTR_variant | Exon 6 of 6 | 1 | NM_001040425.3 | ENSP00000368258.2 | |||
ENSG00000267120 | ENST00000589807.1 | n.*223-51G>C | intron_variant | Intron 6 of 10 | 2 | ENSP00000472696.1 | ||||
IGFLR1 | ENST00000246532.6 | c.-318G>C | upstream_gene_variant | 1 | NM_024660.4 | ENSP00000246532.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250030Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135172
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460776Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726640
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.537G>C (p.W179C) alteration is located in exon 6 (coding exon 6) of the U2AF1L4 gene. This alteration results from a G to C substitution at nucleotide position 537, causing the tryptophan (W) at amino acid position 179 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at