17-7559064-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003808.4(TNFSF13):c.25C>G(p.Leu9Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,558,786 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003808.4 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 |
---|---|---|---|---|---|---|---|
TNFSF13 | NM_003808.4 | c.25C>G | p.Leu9Val | missense_variant | 1/6 | ENST00000338784.9 | |
TNFSF12-TNFSF13 | NM_172089.4 | c.499-560C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFSF13 | ENST00000338784.9 | c.25C>G | p.Leu9Val | missense_variant | 1/6 | 1 | NM_003808.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152240Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000115 AC: 25AN: 217076Hom.: 0 AF XY: 0.000128 AC XY: 15AN XY: 117076
GnomAD4 exome AF: 0.0000995 AC: 140AN: 1406546Hom.: 0 Cov.: 30 AF XY: 0.000105 AC XY: 73AN XY: 693122
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152240Hom.: 0 Cov.: 31 AF XY: 0.000134 AC XY: 10AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.25C>G (p.L9V) alteration is located in exon 1 (coding exon 1) of the TNFSF13 gene. This alteration results from a C to G substitution at nucleotide position 25, causing the leucine (L) at amino acid position 9 to be replaced by a valine (V). 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