9-34690270-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006274.3(CCL19):āc.122A>Cā(p.Tyr41Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,878 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 (ā ).
Frequency
Consequence
NM_006274.3 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 |
---|---|---|---|---|---|---|---|
CCL19 | NM_006274.3 | c.122A>C | p.Tyr41Ser | missense_variant | 2/4 | ENST00000311925.7 | |
PHF24 | XM_047423102.1 | c.48+9053T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCL19 | ENST00000311925.7 | c.122A>C | p.Tyr41Ser | missense_variant | 2/4 | 1 | NM_006274.3 | P2 | |
CCL19 | ENST00000378800.3 | c.122A>C | p.Tyr41Ser | missense_variant | 2/3 | 2 | A2 | ||
CCL19 | ENST00000485502.1 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251292Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135824
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461700Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727160
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 20, 2023 | The c.122A>C (p.Y41S) alteration is located in exon 2 (coding exon 2) of the CCL19 gene. This alteration results from a A to C substitution at nucleotide position 122, causing the tyrosine (Y) at amino acid position 41 to be replaced by a serine (S). 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