16-1494301-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_016111.4(TELO2):āc.20A>Gā(p.Glu7Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 1,612,066 control chromosomes in the GnomAD database, including 55,204 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E7Q) has been classified as Benign.
Frequency
Consequence
NM_016111.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TELO2 | NM_016111.4 | c.20A>G | p.Glu7Gly | missense_variant | 2/21 | ENST00000262319.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TELO2 | ENST00000262319.11 | c.20A>G | p.Glu7Gly | missense_variant | 2/21 | 1 | NM_016111.4 | P1 | |
TELO2 | ENST00000497339.6 | c.20A>G | p.Glu7Gly | missense_variant, NMD_transcript_variant | 2/12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.247 AC: 37473AN: 151414Hom.: 4954 Cov.: 31
GnomAD3 exomes AF: 0.248 AC: 62265AN: 250596Hom.: 8642 AF XY: 0.248 AC XY: 33674AN XY: 135572
GnomAD4 exome AF: 0.255 AC: 372998AN: 1460536Hom.: 50236 Cov.: 36 AF XY: 0.255 AC XY: 184906AN XY: 726490
GnomAD4 genome AF: 0.248 AC: 37518AN: 151530Hom.: 4968 Cov.: 31 AF XY: 0.246 AC XY: 18236AN XY: 74012
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 24, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at