4-182628678-T-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001080477.4(TENM3):c.777T>G(p.Gly259Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0778 in 1,596,730 control chromosomes in the GnomAD database, including 5,494 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001080477.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TENM3 | NM_001080477.4 | c.777T>G | p.Gly259Gly | synonymous_variant | Exon 5 of 28 | ENST00000511685.6 | NP_001073946.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TENM3 | ENST00000511685.6 | c.777T>G | p.Gly259Gly | synonymous_variant | Exon 5 of 28 | 5 | NM_001080477.4 | ENSP00000424226.1 | ||
TENM3 | ENST00000510504.1 | c.351T>G | p.Gly117Gly | synonymous_variant | Exon 3 of 3 | 3 | ENSP00000426914.1 |
Frequencies
GnomAD3 genomes AF: 0.0642 AC: 9772AN: 152102Hom.: 417 Cov.: 31
GnomAD3 exomes AF: 0.0758 AC: 17172AN: 226490Hom.: 811 AF XY: 0.0790 AC XY: 9612AN XY: 121722
GnomAD4 exome AF: 0.0792 AC: 114439AN: 1444510Hom.: 5077 Cov.: 31 AF XY: 0.0805 AC XY: 57673AN XY: 716812
GnomAD4 genome AF: 0.0642 AC: 9778AN: 152220Hom.: 417 Cov.: 31 AF XY: 0.0629 AC XY: 4682AN XY: 74422
ClinVar
Submissions by phenotype
not provided Benign:3
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. -
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at