rs61750079
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PP2PP3_Moderate
The NM_000552.5(VWF):c.4238C>T(p.Pro1413Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,792 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1413Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_000552.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWF | NM_000552.5 | c.4238C>T | p.Pro1413Leu | missense_variant | 28/52 | ENST00000261405.10 | |
VWF | XM_047429501.1 | c.4238C>T | p.Pro1413Leu | missense_variant | 28/52 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWF | ENST00000261405.10 | c.4238C>T | p.Pro1413Leu | missense_variant | 28/52 | 1 | NM_000552.5 | P1 | |
VWF | ENST00000538635.5 | n.421-25246C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152136Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251134Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135736
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461656Hom.: 0 Cov.: 99 AF XY: 0.0000124 AC XY: 9AN XY: 727142
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152136Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74314
ClinVar
Submissions by phenotype
VWF-related condition Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 07, 2022 | The VWF c.4238C>T variant is predicted to result in the amino acid substitution p.Pro1413Leu. This variant has been reported in individuals with Von Willebrand disease 1 (Goodeve et al. 2007. PubMed ID: 16985174; Manderstedt et al. 2018. PubMed ID: 31249928; Dubois et al. 2020. PubMed ID: 33134807). In Manderstedt et al., this variant occurred together with another variant (p.Gly1672Arg), indicating these two variants occur on the same haplotype (Manderstedt et al. 2018. PubMed ID: 31249928). Functional studies using protein expression in cell culture found that the p.Pro1413Leu substitution did not significantly affect protein function (Berber et al. 2016. PubMed ID: 27483487). This variant is reported in 0.0033% of alleles in individuals of South Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/12-6128346-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
not provided Other:1
not provided, no classification provided | literature only | Academic Unit of Haematology, University of Sheffield | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at