GeneBe

chr3-39289016-T-C

Position:

Variant summary

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

The XM_047447538.1(CX3CR1):​c.-10+3776A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 151,838 control chromosomes in the GnomAD database, including 33,522 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 0.66 ( 33522 hom., cov: 30)

Consequence

CX3CR1
XM_047447538.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.943
Variant links:
Genes affected

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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=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CX3CR1XM_047447538.1 linkuse as main transcriptc.-10+3776A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.662
AC:
100380
AN:
151720
Hom.:
33488
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.645
Gnomad AMI
AF:
0.634
Gnomad AMR
AF:
0.750
Gnomad ASJ
AF:
0.630
Gnomad EAS
AF:
0.851
Gnomad SAS
AF:
0.758
Gnomad FIN
AF:
0.654
Gnomad MID
AF:
0.756
Gnomad NFE
AF:
0.633
Gnomad OTH
AF:
0.681
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.662
AC:
100466
AN:
151838
Hom.:
33522
Cov.:
30
AF XY:
0.668
AC XY:
49590
AN XY:
74190
show subpopulations
Gnomad4 AFR
AF:
0.645
Gnomad4 AMR
AF:
0.750
Gnomad4 ASJ
AF:
0.630
Gnomad4 EAS
AF:
0.852
Gnomad4 SAS
AF:
0.757
Gnomad4 FIN
AF:
0.654
Gnomad4 NFE
AF:
0.633
Gnomad4 OTH
AF:
0.684
Alfa
AF:
0.625
Hom.:
3723
Bravo
AF:
0.668
Asia WGS
AF:
0.821
AC:
2857
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.20
DANN
Benign
0.11

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: rs3020452; hg19: chr3-39330507; API