chr4-182680694-T-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001080477.4(TENM3):āc.1791T>Cā(p.Ser597Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 1,592,062 control chromosomes in the GnomAD database, including 131,795 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
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.1791T>C | p.Ser597Ser | synonymous_variant | Exon 10 of 28 | ENST00000511685.6 | NP_001073946.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TENM3 | ENST00000511685.6 | c.1791T>C | p.Ser597Ser | synonymous_variant | Exon 10 of 28 | 5 | NM_001080477.4 | ENSP00000424226.1 | ||
TENM3 | ENST00000502950.1 | n.178T>C | non_coding_transcript_exon_variant | Exon 2 of 15 | 2 | |||||
TENM3 | ENST00000507737.1 | n.323T>C | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.425 AC: 64604AN: 151840Hom.: 14484 Cov.: 31
GnomAD3 exomes AF: 0.453 AC: 105879AN: 233488Hom.: 26157 AF XY: 0.446 AC XY: 56760AN XY: 127126
GnomAD4 exome AF: 0.394 AC: 567317AN: 1440104Hom.: 117280 Cov.: 36 AF XY: 0.397 AC XY: 283854AN XY: 714826
GnomAD4 genome AF: 0.426 AC: 64682AN: 151958Hom.: 14515 Cov.: 31 AF XY: 0.433 AC XY: 32128AN XY: 74262
ClinVar
Submissions by phenotype
not provided Benign:3
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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. -
not specified Benign:1
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Microphthalmia, isolated, with coloboma 9 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at