17-35981408-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004590.4(CCL16):c.13G>A(p.Glu5Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,611,756 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004590.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCL16 | NM_004590.4 | c.13G>A | p.Glu5Lys | missense_variant | 1/3 | ENST00000611905.2 | NP_004581.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCL16 | ENST00000611905.2 | c.13G>A | p.Glu5Lys | missense_variant | 1/3 | 1 | NM_004590.4 | ENSP00000478024 | P1 | |
CCL16 | ENST00000610493.1 | c.13G>A | p.Glu5Lys | missense_variant, NMD_transcript_variant | 1/5 | 5 | ENSP00000478934 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 246682Hom.: 0 AF XY: 0.0000300 AC XY: 4AN XY: 133146
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1459538Hom.: 1 Cov.: 29 AF XY: 0.0000248 AC XY: 18AN XY: 725796
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74420
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 11, 2023 | The c.13G>A (p.E5K) alteration is located in exon 1 (coding exon 1) of the CCL16 gene. This alteration results from a G to A substitution at nucleotide position 13, causing the glutamic acid (E) at amino acid position 5 to be replaced by a lysine (K). 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