rs533306015
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_000214.3(JAG1):c.2418C>T(p.Cys806Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000743 in 1,614,056 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 (★).
Frequency
Consequence
NM_000214.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JAG1 | ENST00000254958.10 | c.2418C>T | p.Cys806Cys | synonymous_variant | Exon 20 of 26 | 1 | NM_000214.3 | ENSP00000254958.4 | ||
JAG1 | ENST00000423891.6 | n.2284C>T | non_coding_transcript_exon_variant | Exon 18 of 25 | 2 | |||||
JAG1 | ENST00000617965.2 | n.3007C>T | non_coding_transcript_exon_variant | Exon 14 of 17 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251386Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135862
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461828Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727210
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74426
ClinVar
Submissions by phenotype
Alagille syndrome due to a JAG1 point mutation Benign:1
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JAG1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at