chr16-57360481-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002990.5(CCL22):c.118T>C(p.Tyr40His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00748 in 1,614,214 control chromosomes in the GnomAD database, including 61 homozygotes. 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 Likely benign (★).
Frequency
Consequence
NM_002990.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCL22 | NM_002990.5 | c.118T>C | p.Tyr40His | missense_variant | 2/3 | ENST00000219235.5 | |
CCL22 | XM_047434449.1 | c.157T>C | p.Tyr53His | missense_variant | 3/4 | ||
CCL22 | XM_047434450.1 | c.118T>C | p.Tyr40His | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCL22 | ENST00000219235.5 | c.118T>C | p.Tyr40His | missense_variant | 2/3 | 1 | NM_002990.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00470 AC: 715AN: 152234Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00521 AC: 1311AN: 251462Hom.: 7 AF XY: 0.00527 AC XY: 716AN XY: 135906
GnomAD4 exome AF: 0.00777 AC: 11353AN: 1461862Hom.: 57 Cov.: 32 AF XY: 0.00771 AC XY: 5610AN XY: 727232
GnomAD4 genome ? AF: 0.00469 AC: 715AN: 152352Hom.: 4 Cov.: 33 AF XY: 0.00448 AC XY: 334AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at