rs707936
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_025258.3(VWA7):c.2499+10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0715 in 1,612,670 control chromosomes in the GnomAD database, including 5,274 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 0.11 ( 1221 hom., cov: 32)
Exomes 𝑓: 0.068 ( 4053 hom. )
Consequence
VWA7
NM_025258.3 intron
NM_025258.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.04
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=-0.85).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWA7 | NM_025258.3 | c.2499+10C>T | intron_variant | ENST00000375688.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWA7 | ENST00000375688.5 | c.2499+10C>T | intron_variant | 5 | NM_025258.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.108 AC: 16477AN: 152148Hom.: 1222 Cov.: 32
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GnomAD3 exomes AF: 0.0802 AC: 19665AN: 245104Hom.: 1012 AF XY: 0.0800 AC XY: 10700AN XY: 133684
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GnomAD4 exome AF: 0.0677 AC: 98797AN: 1460404Hom.: 4053 Cov.: 34 AF XY: 0.0682 AC XY: 49556AN XY: 726428
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GnomAD4 genome ? AF: 0.108 AC: 16478AN: 152266Hom.: 1221 Cov.: 32 AF XY: 0.108 AC XY: 8018AN XY: 74450
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ClinVar
Not reported inComputational scores
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Name
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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