rs138900040
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PM1PP2BP4_StrongBS2_Supporting
The NM_000552.5(VWF):c.3868G>A(p.Glu1290Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,613,982 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_000552.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VWF | ENST00000261405.10 | c.3868G>A | p.Glu1290Lys | missense_variant | Exon 28 of 52 | 1 | NM_000552.5 | ENSP00000261405.5 | ||
VWF | ENST00000539641.1 | n.666G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 3 | |||||
VWF | ENST00000538635.5 | n.421-25616G>A | intron_variant | Intron 5 of 5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.000585 AC: 89AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000207 AC: 52AN: 251084Hom.: 0 AF XY: 0.000228 AC XY: 31AN XY: 135714
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1461666Hom.: 0 Cov.: 38 AF XY: 0.0000564 AC XY: 41AN XY: 727142
GnomAD4 genome AF: 0.000584 AC: 89AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000644 AC XY: 48AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:2
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The VWF c.3868G>A; p.Glu1290Lys variant (rs138900040), to our knowledge, is not reported in the medical literature or gene-specific databases in association with von Willebrand disease. This variant is found in the African population with an overall allele frequency of 0.25% (63/24954 alleles) in the Genome Aggregation Database. The glutamate at codon 1290 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious, although a modeling study incorporating population data and VWF levels suggested the p.Glu1290Lys variant had a low probability of being disease-causing (Cheng 2016). However, given the lack of clinical and functional data, the significance of the p.Glu1290Lys variant is uncertain at this time. References: Cheng Y et al. Group association test using a hidden Markov model. Biostatistics. 2016 Apr;17(2):221-34. -
not provided Uncertain:1
The VWF p.Glu1290Lys variant was not identified in the literature nor was it identified in Cosmic or LOVD 3.0. The variant was identified in dbSNP (ID: rs138900040) and in ClinVar (classified as a VUS by Quest Diagnostics Nichols Institute San Juan Capistrano). The variant was also identified in control databases in 71 of 282484 chromosomes at a frequency of 0.000251 (Genome Aggregation Database Feb 27, 2017) and was observed in the following populations: African in 63 of 24954 chromosomes (freq: 0.002525), Latino in 5 of 35440 chromosomes (freq: 0.000141), South Asian in 2 of 30616 chromosomes (freq: 0.000065) and European (non-Finnish) in 1 of 128814 chromosomes (freq: 0.000008), while the variant was not observed in the Ashkenazi Jewish, East Asian, European (Finnish), and Other populations. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. The p.Glu1290 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at