chr15-81279712-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_172217.5(IL16):c.1019C>T(p.Ser340Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000396 in 1,614,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_172217.5 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 |
---|---|---|---|---|---|---|---|
IL16 | NM_172217.5 | c.1019C>T | p.Ser340Leu | missense_variant | 8/19 | ENST00000683961.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL16 | ENST00000683961.1 | c.1019C>T | p.Ser340Leu | missense_variant | 8/19 | NM_172217.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000521 AC: 13AN: 249466Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135338
GnomAD4 exome AF: 0.0000369 AC: 54AN: 1461880Hom.: 0 Cov.: 32 AF XY: 0.0000358 AC XY: 26AN XY: 727236
GnomAD4 genome ? AF: 0.0000656 AC: 10AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.1019C>T (p.S340L) alteration is located in exon 7 (coding exon 7) of the IL16 gene. This alteration results from a C to T substitution at nucleotide position 1019, causing the serine (S) at amino acid position 340 to be replaced by a leucine (L). 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