3-169765003-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NR_001566.3(TERC):n.58G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00479 in 765,446 control chromosomes in the GnomAD database, including 76 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NR_001566.3 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TERC | NR_001566.3 | n.58G>A | non_coding_transcript_exon_variant | Exon 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0159 AC: 2420AN: 152238Hom.: 52 Cov.: 32
GnomAD3 exomes AF: 0.00378 AC: 875AN: 231422Hom.: 17 AF XY: 0.00299 AC XY: 382AN XY: 127830
GnomAD4 exome AF: 0.00203 AC: 1242AN: 613090Hom.: 24 Cov.: 0 AF XY: 0.00154 AC XY: 515AN XY: 335118
GnomAD4 genome AF: 0.0159 AC: 2423AN: 152356Hom.: 52 Cov.: 32 AF XY: 0.0153 AC XY: 1137AN XY: 74502
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:2
c.58G>A in TERC: This variant is not expected to have clinical significance beca use it has been identified in 5.6% (1269/22484) of African chromosomes by the Ge nome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs113 4787931). In addition, in vitro functional assays of telomerase activity show no loss of function with this variant (Ly 2003, Marrone 2004). ACMG/AMP Criteria a pplied: BA1, BS3. -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Aplastic anemia Pathogenic:1
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Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 2 Pathogenic:1
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Dyskeratosis congenita, autosomal dominant 1 Benign:1
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Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 2;C4551974:Dyskeratosis congenita, autosomal dominant 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at