17-40478583-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_032865.6(TNS4):c.1976G>A(p.Arg659Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,614,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032865.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNS4 | NM_032865.6 | c.1976G>A | p.Arg659Gln | missense_variant | Exon 11 of 13 | ENST00000254051.11 | NP_116254.4 | |
TNS4 | XM_047436949.1 | c.2312G>A | p.Arg771Gln | missense_variant | Exon 11 of 13 | XP_047292905.1 | ||
TNS4 | XM_005257744.2 | c.1973G>A | p.Arg658Gln | missense_variant | Exon 11 of 13 | XP_005257801.1 | ||
TNS4 | XM_017025236.2 | c.1898G>A | p.Arg633Gln | missense_variant | Exon 10 of 12 | XP_016880725.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNS4 | ENST00000254051.11 | c.1976G>A | p.Arg659Gln | missense_variant | Exon 11 of 13 | 1 | NM_032865.6 | ENSP00000254051.6 | ||
TNS4 | ENST00000394072.7 | n.242G>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 1 | |||||
TNS4 | ENST00000582747.1 | c.65G>A | p.Arg22Gln | missense_variant | Exon 1 of 2 | 3 | ENSP00000463456.1 | |||
TNS4 | ENST00000497303.1 | n.405G>A | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251256Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135782
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461782Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727198
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1976G>A (p.R659Q) alteration is located in exon 11 (coding exon 10) of the TNS4 gene. This alteration results from a G to A substitution at nucleotide position 1976, causing the arginine (R) at amino acid position 659 to be replaced by a glutamine (Q). 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