4-26320822-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The ENST00000361572.10(RBPJ):c.59+7T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000071 in 1,407,670 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000361572.10 splice_region, intron
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 |
---|---|---|---|---|---|---|---|
RBPJ | NM_001374400.1 | c.59+7T>C | splice_region_variant, intron_variant | ||||
RBPJ | NM_001374401.1 | c.-166-41624T>C | intron_variant | ||||
RBPJ | NM_001379406.1 | c.-167+934T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBPJ | ENST00000348160.9 | c.-393T>C | 5_prime_UTR_variant | 1/12 | 1 | A1 | |||
RBPJ | ENST00000345843.8 | c.-47+934T>C | intron_variant | 1 | |||||
RBPJ | ENST00000361572.10 | c.59+7T>C | splice_region_variant, intron_variant | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 7.10e-7 AC: 1AN: 1407670Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 694816
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 19, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at