rs588019

Variant summary

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

The NM_001838.4(CCR7):​c.60+38C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0725 in 1,594,012 control chromosomes in the GnomAD database, including 4,654 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 0.053 ( 268 hom., cov: 32)
Exomes 𝑓: 0.075 ( 4386 hom. )

Consequence

CCR7
NM_001838.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00300
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=-0.8).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0861 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CCR7NM_001838.4 linkuse as main transcriptc.60+38C>T intron_variant ENST00000246657.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCR7ENST00000246657.2 linkuse as main transcriptc.60+38C>T intron_variant 1 NM_001838.4 P1
CCR7ENST00000579344.1 linkuse as main transcriptc.42+38C>T intron_variant 1
CCR7ENST00000578085.1 linkuse as main transcriptc.-129-3037C>T intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0535
AC:
8141
AN:
152148
Hom.:
269
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0136
Gnomad AMI
AF:
0.0716
Gnomad AMR
AF:
0.0509
Gnomad ASJ
AF:
0.0654
Gnomad EAS
AF:
0.0630
Gnomad SAS
AF:
0.0943
Gnomad FIN
AF:
0.0550
Gnomad MID
AF:
0.0222
Gnomad NFE
AF:
0.0740
Gnomad OTH
AF:
0.0464
GnomAD3 exomes
AF:
0.0656
AC:
16418
AN:
250234
Hom.:
660
AF XY:
0.0685
AC XY:
9265
AN XY:
135238
show subpopulations
Gnomad AFR exome
AF:
0.0127
Gnomad AMR exome
AF:
0.0420
Gnomad ASJ exome
AF:
0.0659
Gnomad EAS exome
AF:
0.0603
Gnomad SAS exome
AF:
0.105
Gnomad FIN exome
AF:
0.0527
Gnomad NFE exome
AF:
0.0733
Gnomad OTH exome
AF:
0.0604
GnomAD4 exome
AF:
0.0745
AC:
107438
AN:
1441746
Hom.:
4386
Cov.:
27
AF XY:
0.0751
AC XY:
53949
AN XY:
718526
show subpopulations
Gnomad4 AFR exome
AF:
0.0110
Gnomad4 AMR exome
AF:
0.0432
Gnomad4 ASJ exome
AF:
0.0639
Gnomad4 EAS exome
AF:
0.0567
Gnomad4 SAS exome
AF:
0.101
Gnomad4 FIN exome
AF:
0.0540
Gnomad4 NFE exome
AF:
0.0778
Gnomad4 OTH exome
AF:
0.0722
GnomAD4 genome
AF:
0.0534
AC:
8138
AN:
152266
Hom.:
268
Cov.:
32
AF XY:
0.0540
AC XY:
4018
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.0136
Gnomad4 AMR
AF:
0.0508
Gnomad4 ASJ
AF:
0.0654
Gnomad4 EAS
AF:
0.0633
Gnomad4 SAS
AF:
0.0932
Gnomad4 FIN
AF:
0.0550
Gnomad4 NFE
AF:
0.0740
Gnomad4 OTH
AF:
0.0473
Alfa
AF:
0.0486
Hom.:
87
Bravo
AF:
0.0485
Asia WGS
AF:
0.0980
AC:
342
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
2.7
DANN
Benign
0.76

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs588019; hg19: chr17-38715107; API