rs373488315
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_198253.3(TERT):c.2383-5C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,609,632 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_198253.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TERT | NM_198253.3 | c.2383-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000310581.10 | |||
TERT | NM_001193376.3 | c.2383-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
TERT | NR_149162.3 | n.2366-2576C>T | intron_variant, non_coding_transcript_variant | ||||
TERT | NR_149163.3 | n.2330-2576C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TERT | ENST00000310581.10 | c.2383-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_198253.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152268Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247148Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134630
GnomAD4 exome AF: 0.0000350 AC: 51AN: 1457364Hom.: 0 Cov.: 30 AF XY: 0.0000331 AC XY: 24AN XY: 725094
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152268Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74390
ClinVar
Submissions by phenotype
Idiopathic Pulmonary Fibrosis;C3151443:Dyskeratosis congenita, autosomal dominant 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at