4-182324110-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PM2PP2BP4_StrongBS1_Supporting
The NM_001080477.4(TENM3):āc.90T>Gā(p.Asn30Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,886 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001080477.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENM3 | NM_001080477.4 | c.90T>G | p.Asn30Lys | missense_variant | 2/28 | ENST00000511685.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENM3 | ENST00000511685.6 | c.90T>G | p.Asn30Lys | missense_variant | 2/28 | 5 | NM_001080477.4 | P1 | |
TENM3 | ENST00000513201.1 | n.340T>G | non_coding_transcript_exon_variant | 2/4 | 1 | ||||
TENM3 | ENST00000512480.5 | c.90T>G | p.Asn30Lys | missense_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152064Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000843 AC: 21AN: 249224Hom.: 0 AF XY: 0.0000962 AC XY: 13AN XY: 135186
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461704Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727136
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74402
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 08, 2022 | The c.90T>G (p.N30K) alteration is located in exon 1 (coding exon 1) of the TENM3 gene. This alteration results from a T to G substitution at nucleotide position 90, causing the asparagine (N) at amino acid position 30 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at