9-35704793-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP2
The NM_006289.4(TLN1):c.5756G>A(p.Arg1919Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000112 in 1,613,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1919W) has been classified as Likely benign.
Frequency
Consequence
NM_006289.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLN1 | NM_006289.4 | c.5756G>A | p.Arg1919Gln | missense_variant | 44/57 | ENST00000314888.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLN1 | ENST00000314888.10 | c.5756G>A | p.Arg1919Gln | missense_variant | 44/57 | 1 | NM_006289.4 | P1 | |
TLN1 | ENST00000706939.1 | c.5807G>A | p.Arg1936Gln | missense_variant | 45/58 | ||||
TLN1 | ENST00000464379.5 | n.106-11G>A | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 3 | |||||
TLN1 | ENST00000486788.2 | n.376-295G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251130Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135714
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461736Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 727162
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2022 | The c.5756G>A (p.R1919Q) alteration is located in exon 44 (coding exon 43) of the TLN1 gene. This alteration results from a G to A substitution at nucleotide position 5756, causing the arginine (R) at amino acid position 1919 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