rs759022807
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_000214.3(JAG1):c.3048+30_3048+32del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000247 in 1,613,732 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00024 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00025 ( 0 hom. )
Consequence
JAG1
NM_000214.3 intron
NM_000214.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0210
Genes affected
JAG1 (HGNC:6188): (jagged canonical Notch ligand 1) The jagged 1 protein encoded by JAG1 is the human homolog of the Drosophilia jagged protein. Human jagged 1 is the ligand for the receptor notch 1, the latter is involved in signaling processes. Mutations that alter the jagged 1 protein cause Alagille syndrome. Jagged 1 signalling through notch 1 has also been shown to play a role in hematopoiesis. [provided by RefSeq, Nov 2019]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 20-10641080-GAAT-G is Benign according to our data. Variant chr20-10641080-GAAT-G is described in ClinVar as [Likely_benign]. Clinvar id is 255558.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000243 (37/152140) while in subpopulation NFE AF= 0.000514 (35/68032). AF 95% confidence interval is 0.000379. There are 0 homozygotes in gnomad4. There are 14 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 37 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JAG1 | NM_000214.3 | c.3048+30_3048+32del | intron_variant | ENST00000254958.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JAG1 | ENST00000254958.10 | c.3048+30_3048+32del | intron_variant | 1 | NM_000214.3 | P1 | |||
JAG1 | ENST00000617357.1 | n.194_196del | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
JAG1 | ENST00000423891.6 | n.2914+30_2914+32del | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000243 AC: 37AN: 152140Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000219 AC: 55AN: 251032Hom.: 0 AF XY: 0.000228 AC XY: 31AN XY: 135674
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GnomAD4 exome AF: 0.000247 AC: 361AN: 1461592Hom.: 0 AF XY: 0.000245 AC XY: 178AN XY: 727106
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GnomAD4 genome ? AF: 0.000243 AC: 37AN: 152140Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74320
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at