chr5-1294764-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_198253.3(TERT):c.219+7C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000575 in 1,392,250 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
NM_198253.3 splice_region, intron
Scores
Clinical Significance
Conservation
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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.219+7C>A | splice_region_variant, intron_variant | ENST00000310581.10 | |||
TERT | NM_001193376.3 | c.219+7C>A | splice_region_variant, intron_variant | ||||
TERT | NR_149162.3 | n.298+7C>A | splice_region_variant, intron_variant, non_coding_transcript_variant | ||||
TERT | NR_149163.3 | n.298+7C>A | splice_region_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TERT | ENST00000310581.10 | c.219+7C>A | splice_region_variant, intron_variant | 1 | NM_198253.3 | P2 | |||
TERT | ENST00000334602.10 | c.219+7C>A | splice_region_variant, intron_variant | 1 | A2 | ||||
TERT | ENST00000460137.6 | c.219+7C>A | splice_region_variant, intron_variant, NMD_transcript_variant | 1 | |||||
TERT | ENST00000656021.1 | c.219+7C>A | splice_region_variant, intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.00000707 AC: 1AN: 141468Hom.: 0 AF XY: 0.0000127 AC XY: 1AN XY: 78526
GnomAD4 exome AF: 0.00000575 AC: 8AN: 1392250Hom.: 0 Cov.: 35 AF XY: 0.00000436 AC XY: 3AN XY: 688434
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Idiopathic Pulmonary Fibrosis;C3151443:Dyskeratosis congenita, autosomal dominant 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at