chr15-62675274-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015059.3(TLN2):c.910C>T(p.Leu304Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,890 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. L304L) has been classified as Likely benign.
Frequency
Consequence
NM_015059.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLN2 | NM_015059.3 | c.910C>T | p.Leu304Phe | missense_variant | 11/59 | ENST00000636159.2 | |
LOC105370855 | XR_007064673.1 | n.530-6202G>A | intron_variant, non_coding_transcript_variant | ||||
TLN2 | NM_001394547.1 | c.910C>T | p.Leu304Phe | missense_variant | 10/58 | ||
LOC105370855 | XR_007064672.1 | n.461-6202G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLN2 | ENST00000636159.2 | c.910C>T | p.Leu304Phe | missense_variant | 11/59 | 5 | NM_015059.3 | P1 | |
TLN2 | ENST00000561311.5 | c.910C>T | p.Leu304Phe | missense_variant | 10/58 | 5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251472Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135908
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461890Hom.: 0 Cov.: 36 AF XY: 0.00000138 AC XY: 1AN XY: 727246
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.910C>T (p.L304F) alteration is located in exon 8 (coding exon 8) of the TLN2 gene. This alteration results from a C to T substitution at nucleotide position 910, causing the leucine (L) at amino acid position 304 to be replaced by a phenylalanine (F). 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