chr9-34709583-T-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_002989.4(CCL21):c.288A>G(p.Pro96=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00109 in 1,614,132 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0055 ( 10 hom., cov: 32)
Exomes 𝑓: 0.00063 ( 7 hom. )
Consequence
CCL21
NM_002989.4 synonymous
NM_002989.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0240
Genes affected
CCL21 (HGNC:10620): (C-C motif chemokine ligand 21) This antimicrobial gene is one of several CC cytokine genes clustered on the p-arm of chromosome 9. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. Similar to other chemokines the protein encoded by this gene inhibits hemopoiesis and stimulates chemotaxis. This protein is chemotactic in vitro for thymocytes and activated T cells, but not for B cells, macrophages, or neutrophils. The cytokine encoded by this gene may also play a role in mediating homing of lymphocytes to secondary lymphoid organs. It is a high affinity functional ligand for chemokine receptor 7 that is expressed on T and B lymphocytes and a known receptor for another member of the cytokine family (small inducible cytokine A19). [provided by RefSeq, Sep 2014]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 9-34709583-T-C is Benign according to our data. Variant chr9-34709583-T-C is described in ClinVar as [Benign]. Clinvar id is 792124.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.024 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00548 (835/152258) while in subpopulation AFR AF= 0.0189 (786/41536). AF 95% confidence interval is 0.0178. There are 10 homozygotes in gnomad4. There are 384 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCL21 | NM_002989.4 | c.288A>G | p.Pro96= | synonymous_variant | 3/4 | ENST00000259607.7 | |
PHF24 | XM_047423102.1 | c.133+6545T>C | intron_variant | ||||
PHF24 | XM_047423103.1 | c.70+6545T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCL21 | ENST00000259607.7 | c.288A>G | p.Pro96= | synonymous_variant | 3/4 | 1 | NM_002989.4 | P1 | |
ENST00000664167.1 | n.86+6545T>C | intron_variant, non_coding_transcript_variant | |||||||
CCL21 | ENST00000378792.1 | c.288A>G | p.Pro96= | synonymous_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00546 AC: 830AN: 152140Hom.: 10 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
830
AN:
152140
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00141 AC: 355AN: 251318Hom.: 1 AF XY: 0.00108 AC XY: 147AN XY: 135842
GnomAD3 exomes
AF:
AC:
355
AN:
251318
Hom.:
AF XY:
AC XY:
147
AN XY:
135842
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000631 AC: 922AN: 1461874Hom.: 7 Cov.: 31 AF XY: 0.000572 AC XY: 416AN XY: 727240
GnomAD4 exome
AF:
AC:
922
AN:
1461874
Hom.:
Cov.:
31
AF XY:
AC XY:
416
AN XY:
727240
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00548 AC: 835AN: 152258Hom.: 10 Cov.: 32 AF XY: 0.00516 AC XY: 384AN XY: 74454
GnomAD4 genome
?
AF:
AC:
835
AN:
152258
Hom.:
Cov.:
32
AF XY:
AC XY:
384
AN XY:
74454
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 28, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at