6-32197424-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2
The NM_004557.4(NOTCH4):c.4927C>T(p.Arg1643Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000306 in 1,547,108 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 Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_004557.4 stop_gained
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 | UniProt |
---|---|---|---|---|---|---|---|
NOTCH4 | NM_004557.4 | c.4927C>T | p.Arg1643Ter | stop_gained | 27/30 | ENST00000375023.3 | |
NOTCH4 | NR_134949.2 | n.4635C>T | non_coding_transcript_exon_variant | 27/30 | |||
NOTCH4 | NR_134950.2 | n.4533C>T | non_coding_transcript_exon_variant | 26/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOTCH4 | ENST00000375023.3 | c.4927C>T | p.Arg1643Ter | stop_gained | 27/30 | 1 | NM_004557.4 | P1 | |
NOTCH4 | ENST00000474612.1 | n.3588C>T | non_coding_transcript_exon_variant | 7/10 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000203 AC: 40AN: 196916Hom.: 0 AF XY: 0.000162 AC XY: 17AN XY: 105192
GnomAD4 exome AF: 0.000318 AC: 443AN: 1394902Hom.: 0 Cov.: 32 AF XY: 0.000276 AC XY: 190AN XY: 687432
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74364
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 05, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at