rs762729988
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PP2PP3BP6_ModerateBS2
The NM_017617.5(NOTCH1):c.2425G>A(p.Asp809Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000548 in 1,459,154 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 Benign (★). Synonymous variant affecting the same amino acid position (i.e. D809D) has been classified as Likely benign.
Frequency
Consequence
NM_017617.5 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 |
---|---|---|---|---|---|---|---|
NOTCH1 | NM_017617.5 | c.2425G>A | p.Asp809Asn | missense_variant | 15/34 | ENST00000651671.1 | |
LOC124902310 | XR_007061865.1 | n.507+3084C>T | intron_variant, non_coding_transcript_variant | ||||
NOTCH1 | XM_011518717.3 | c.1702G>A | p.Asp568Asn | missense_variant | 12/31 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOTCH1 | ENST00000651671.1 | c.2425G>A | p.Asp809Asn | missense_variant | 15/34 | NM_017617.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000805 AC: 2AN: 248326Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135202
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1459154Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 725840
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Adams-Oliver syndrome 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at