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rs2107538

Variant summary

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

The ENST00000605548.1(null):n.153-3606C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 163,666 control chromosomes in the GnomAD database, including 6,602 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 0.27 ( 6325 hom., cov: 32)
Exomes 𝑓: 0.19 ( 277 hom. )

Consequence


ENST00000605548.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.426
Variant links:
Genes affected
CCL5 (HGNC:10632): (C-C motif chemokine ligand 5) This gene is one of several chemokine genes clustered on the q-arm of chromosome 17. Chemokines form a superfamily of secreted proteins involved in immunoregulatory and inflammatory processes. The superfamily is divided into four subfamilies based on the arrangement of the N-terminal cysteine residues of the mature peptide. This chemokine, a member of the CC subfamily, functions as a chemoattractant for blood monocytes, memory T helper cells and eosinophils. It causes the release of histamine from basophils and activates eosinophils. This cytokine is one of the major HIV-suppressive factors produced by CD8+ cells. It functions as one of the natural ligands for the chemokine receptor chemokine (C-C motif) receptor 5 (CCR5), and it suppresses in vitro replication of the R5 strains of HIV-1, which use CCR5 as a coreceptor. Alternative splicing results in multiple transcript variants that encode different isoforms. [provided by RefSeq, Jul 2013]

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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=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105371745XR_007065724.1 linkuse as main transcriptn.148-3606C>T intron_variant, non_coding_transcript_variant
LOC105371745XR_934699.2 linkuse as main transcriptn.148-3606C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000605548.1 linkuse as main transcriptn.153-3606C>T intron_variant, non_coding_transcript_variant 3
CCL5ENST00000605509.2 linkuse as main transcriptc.-65G>A 5_prime_UTR_variant 1/43 P1

Frequencies

GnomAD3 genomes
AF:
0.265
AC:
40212
AN:
151968
Hom.:
6290
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.433
Gnomad AMI
AF:
0.226
Gnomad AMR
AF:
0.235
Gnomad ASJ
AF:
0.189
Gnomad EAS
AF:
0.343
Gnomad SAS
AF:
0.302
Gnomad FIN
AF:
0.178
Gnomad MID
AF:
0.190
Gnomad NFE
AF:
0.180
Gnomad OTH
AF:
0.231
GnomAD4 exome
AF:
0.191
AC:
2210
AN:
11580
Hom.:
277
Cov.:
0
AF XY:
0.192
AC XY:
1129
AN XY:
5884
show subpopulations
Gnomad4 AFR exome
AF:
0.368
Gnomad4 AMR exome
AF:
0.225
Gnomad4 ASJ exome
AF:
0.195
Gnomad4 EAS exome
AF:
0.328
Gnomad4 SAS exome
AF:
0.243
Gnomad4 FIN exome
AF:
0.0900
Gnomad4 NFE exome
AF:
0.155
Gnomad4 OTH exome
AF:
0.174
GnomAD4 genome
AF:
0.265
AC:
40309
AN:
152086
Hom.:
6325
Cov.:
32
AF XY:
0.265
AC XY:
19740
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.434
Gnomad4 AMR
AF:
0.235
Gnomad4 ASJ
AF:
0.189
Gnomad4 EAS
AF:
0.342
Gnomad4 SAS
AF:
0.303
Gnomad4 FIN
AF:
0.178
Gnomad4 NFE
AF:
0.180
Gnomad4 OTH
AF:
0.232
Alfa
AF:
0.226
Hom.:
821
Bravo
AF:
0.276
Asia WGS
AF:
0.308
AC:
1070
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
1.7
Dann
Benign
0.79

Splicing

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: rs2107538; hg19: chr17-34207780; API