chr9-115026688-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002160.4(TNC):c.6177C>A(p.Asp2059Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,516 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002160.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNC | NM_002160.4 | c.6177C>A | p.Asp2059Glu | missense_variant | 26/28 | ENST00000350763.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNC | ENST00000350763.9 | c.6177C>A | p.Asp2059Glu | missense_variant | 26/28 | 1 | NM_002160.4 | P1 | |
DELEC1 | ENST00000649121.1 | n.78+57027G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461516Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727050
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 23, 2023 | The c.6177C>A (p.D2059E) alteration is located in exon 26 (coding exon 25) of the TNC gene. This alteration results from a C to A substitution at nucleotide position 6177, causing the aspartic acid (D) at amino acid position 2059 to be replaced by a glutamic acid (E). 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