16-22116850-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173615.5(VWA3A):c.907G>A(p.Asp303Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,612,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173615.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VWA3A | NM_173615.5 | c.907G>A | p.Asp303Asn | missense_variant | 10/34 | ENST00000389398.10 | NP_775886.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VWA3A | ENST00000389398.10 | c.907G>A | p.Asp303Asn | missense_variant | 10/34 | 5 | NM_173615.5 | ENSP00000374049 | P1 | |
VWA3A | ENST00000568328.5 | c.907G>A | p.Asp303Asn | missense_variant | 10/23 | 1 | ENSP00000457770 | |||
VWA3A | ENST00000566668.1 | n.1101G>A | non_coding_transcript_exon_variant | 9/20 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000805 AC: 2AN: 248396Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134870
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460592Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 726642
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2023 | The c.907G>A (p.D303N) alteration is located in exon 10 (coding exon 10) of the VWA3A gene. This alteration results from a G to A substitution at nucleotide position 907, causing the aspartic acid (D) at amino acid position 303 to be replaced by an asparagine (N). 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