rs61751553
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_017617.5(NOTCH1):c.2049G>T(p.Ala683=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,102 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A683A) has been classified as Likely benign.
Frequency
Consequence
NM_017617.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOTCH1 | NM_017617.5 | c.2049G>T | p.Ala683= | synonymous_variant | 13/34 | ENST00000651671.1 | NP_060087.3 | |
LOC124902310 | XR_007061865.1 | n.507+4689C>A | intron_variant, non_coding_transcript_variant | |||||
NOTCH1 | XM_011518717.3 | c.1326G>T | p.Ala442= | synonymous_variant | 10/31 | XP_011517019.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOTCH1 | ENST00000651671.1 | c.2049G>T | p.Ala683= | synonymous_variant | 13/34 | NM_017617.5 | ENSP00000498587 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000408 AC: 1AN: 244950Hom.: 0 AF XY: 0.00000748 AC XY: 1AN XY: 133696
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460102Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726326
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at