17-40561644-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001838.4(CCR7):​c.11-2702A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,068 control chromosomes in the GnomAD database, including 6,432 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 6432 hom., cov: 32)

Consequence

CCR7
NM_001838.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0610
Variant links:
Genes affected
CCR7 (HGNC:1608): (C-C motif chemokine receptor 7) The protein encoded by this gene is a member of the G protein-coupled receptor family. This receptor was identified as a gene induced by the Epstein-Barr virus (EBV), and is thought to be a mediator of EBV effects on B lymphocytes. This receptor is expressed in various lymphoid tissues and activates B and T lymphocytes. It has been shown to control the migration of memory T cells to inflamed tissues, as well as stimulate dendritic cell maturation. The chemokine (C-C motif) ligand 19 (CCL19/ECL) has been reported to be a specific ligand of this receptor. Signals mediated by this receptor regulate T cell homeostasis in lymph nodes, and may also function in the activation and polarization of T cells, and in chronic inflammation pathogenesis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CCR7NM_001838.4 linkuse as main transcriptc.11-2702A>G intron_variant ENST00000246657.2 NP_001829.1 P32248A0N0Q0
CCR7NM_001301714.2 linkuse as main transcriptc.-130+3756A>G intron_variant NP_001288643.1 P32248

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CCR7ENST00000246657.2 linkuse as main transcriptc.11-2702A>G intron_variant 1 NM_001838.4 ENSP00000246657.2 P32248
CCR7ENST00000578085.1 linkuse as main transcriptc.-130+3756A>G intron_variant 3 ENSP00000463075.1 J3KTN5

Frequencies

GnomAD3 genomes
AF:
0.172
AC:
26088
AN:
151950
Hom.:
6395
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.551
Gnomad AMI
AF:
0.0573
Gnomad AMR
AF:
0.0820
Gnomad ASJ
AF:
0.0107
Gnomad EAS
AF:
0.0146
Gnomad SAS
AF:
0.00954
Gnomad FIN
AF:
0.00764
Gnomad MID
AF:
0.0570
Gnomad NFE
AF:
0.0222
Gnomad OTH
AF:
0.127
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.172
AC:
26181
AN:
152068
Hom.:
6432
Cov.:
32
AF XY:
0.166
AC XY:
12353
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.552
Gnomad4 AMR
AF:
0.0818
Gnomad4 ASJ
AF:
0.0107
Gnomad4 EAS
AF:
0.0147
Gnomad4 SAS
AF:
0.00934
Gnomad4 FIN
AF:
0.00764
Gnomad4 NFE
AF:
0.0222
Gnomad4 OTH
AF:
0.125
Alfa
AF:
0.0351
Hom.:
610
Bravo
AF:
0.197
Asia WGS
AF:
0.0500
AC:
176
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.8
DANN
Benign
0.64

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3136687; hg19: chr17-38717896; API