chr9-136496170-C-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_017617.5(NOTCH1):āc.7569G>Cā(p.Ser2523=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000617 in 1,457,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. S2523S) has been classified as Likely benign.
Frequency
Consequence
NM_017617.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOTCH1 | NM_017617.5 | c.7569G>C | p.Ser2523= | synonymous_variant | 34/34 | ENST00000651671.1 | |
NOTCH1 | XM_011518717.3 | c.6846G>C | p.Ser2282= | synonymous_variant | 31/31 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOTCH1 | ENST00000651671.1 | c.7569G>C | p.Ser2523= | synonymous_variant | 34/34 | NM_017617.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000125 AC: 3AN: 240264Hom.: 0 AF XY: 0.0000230 AC XY: 3AN XY: 130650
GnomAD4 exome AF: 0.00000617 AC: 9AN: 1457970Hom.: 0 Cov.: 31 AF XY: 0.00000966 AC XY: 7AN XY: 724942
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Adams-Oliver syndrome 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 13, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at