rs3130490
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_025258.3(VWA7):c.1088-1230C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0766 in 152,292 control chromosomes in the GnomAD database, including 560 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.077 ( 560 hom., cov: 31)
Exomes 𝑓: 0.0082 ( 0 hom. )
Consequence
VWA7
NM_025258.3 intron
NM_025258.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0590
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWA7 | NM_025258.3 | c.1088-1230C>A | intron_variant | ENST00000375688.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWA7 | ENST00000375688.5 | c.1088-1230C>A | intron_variant | 5 | NM_025258.3 | P1 | |||
VWA7 | ENST00000487013.1 | n.535C>A | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
VWA7 | ENST00000467576.1 | n.951-1230C>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0767 AC: 11664AN: 152052Hom.: 560 Cov.: 31
GnomAD3 genomes
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31
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GnomAD4 exome AF: 0.00820 AC: 1AN: 122Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 80
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GnomAD4 genome ? AF: 0.0767 AC: 11665AN: 152170Hom.: 560 Cov.: 31 AF XY: 0.0712 AC XY: 5300AN XY: 74406
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at