7-12356204-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001135924.3(VWDE):c.3652G>A(p.Asp1218Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000387 in 1,551,410 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001135924.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWDE | NM_001135924.3 | c.3652G>A | p.Asp1218Asn | missense_variant | 18/29 | ENST00000275358.8 | |
VWDE | NM_001346972.2 | c.3307G>A | p.Asp1103Asn | missense_variant | 16/27 | ||
VWDE | NM_001346973.2 | c.2842G>A | p.Asp948Asn | missense_variant | 16/27 | ||
VWDE | NR_144534.2 | n.3801G>A | non_coding_transcript_exon_variant | 18/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWDE | ENST00000275358.8 | c.3652G>A | p.Asp1218Asn | missense_variant | 18/29 | 5 | NM_001135924.3 | P1 | |
VWDE | ENST00000452576.6 | c.3652G>A | p.Asp1218Asn | missense_variant, NMD_transcript_variant | 18/30 | 1 | |||
VWDE | ENST00000644150.1 | c.127G>A | p.Asp43Asn | missense_variant | 1/3 | ||||
VWDE | ENST00000521169.5 | c.*2030G>A | 3_prime_UTR_variant, NMD_transcript_variant | 15/26 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000192 AC: 3AN: 156540Hom.: 0 AF XY: 0.0000241 AC XY: 2AN XY: 82970
GnomAD4 exome AF: 0.00000357 AC: 5AN: 1399352Hom.: 0 Cov.: 35 AF XY: 0.00000435 AC XY: 3AN XY: 690184
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74270
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at