NM_198253.3:c.1449C>T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_198253.3(TERT):c.1449C>T(p.Asn483Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,611,790 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_198253.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TERT | NM_198253.3 | c.1449C>T | p.Asn483Asn | synonymous_variant | Exon 2 of 16 | ENST00000310581.10 | NP_937983.2 | |
TERT | NM_001193376.3 | c.1449C>T | p.Asn483Asn | synonymous_variant | Exon 2 of 15 | NP_001180305.1 | ||
TERT | NR_149162.3 | n.1528C>T | non_coding_transcript_exon_variant | Exon 2 of 13 | ||||
TERT | NR_149163.3 | n.1528C>T | non_coding_transcript_exon_variant | Exon 2 of 13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TERT | ENST00000310581.10 | c.1449C>T | p.Asn483Asn | synonymous_variant | Exon 2 of 16 | 1 | NM_198253.3 | ENSP00000309572.5 | ||
TERT | ENST00000334602.10 | c.1449C>T | p.Asn483Asn | synonymous_variant | Exon 2 of 15 | 1 | ENSP00000334346.6 | |||
TERT | ENST00000460137.6 | n.1449C>T | non_coding_transcript_exon_variant | Exon 2 of 13 | 1 | ENSP00000425003.1 | ||||
TERT | ENST00000656021.1 | n.1449C>T | non_coding_transcript_exon_variant | Exon 2 of 17 | ENSP00000499759.1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152256Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000899 AC: 22AN: 244626Hom.: 0 AF XY: 0.0000676 AC XY: 9AN XY: 133192
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1459534Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 726030
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152256Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74388
ClinVar
Submissions by phenotype
not specified Benign:1
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Idiopathic Pulmonary Fibrosis;C3151443:Dyskeratosis congenita, autosomal dominant 2 Benign:1
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Dyskeratosis congenita Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at