9-34691127-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006274.3(CCL19):āc.13C>Gā(p.Leu5Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000093 in 1,613,460 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_006274.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCL19 | NM_006274.3 | c.13C>G | p.Leu5Val | missense_variant | 1/4 | ENST00000311925.7 | |
PHF24 | XM_047423102.1 | c.48+9910G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCL19 | ENST00000311925.7 | c.13C>G | p.Leu5Val | missense_variant | 1/4 | 1 | NM_006274.3 | P2 | |
CCL19 | ENST00000378800.3 | c.13C>G | p.Leu5Val | missense_variant | 1/3 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152240Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000644 AC: 16AN: 248462Hom.: 0 AF XY: 0.0000744 AC XY: 10AN XY: 134442
GnomAD4 exome AF: 0.0000944 AC: 138AN: 1461102Hom.: 0 Cov.: 30 AF XY: 0.0000991 AC XY: 72AN XY: 726782
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152358Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 4AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2023 | The c.13C>G (p.L5V) alteration is located in exon 1 (coding exon 1) of the CCL19 gene. This alteration results from a C to G substitution at nucleotide position 13, causing the leucine (L) at amino acid position 5 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