GeneBe

3-39284792-T-G

Position:

Variant summary

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

The XM_047447538.1(CX3CR1):​c.-10+8000A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,930 control chromosomes in the GnomAD database, including 7,591 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 0.28 ( 7591 hom., cov: 32)

Consequence

CX3CR1
XM_047447538.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.442
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CX3CR1XM_047447538.1 linkuse as main transcriptc.-10+8000A>C intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.285
AC:
43214
AN:
151814
Hom.:
7592
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.130
Gnomad AMI
AF:
0.359
Gnomad AMR
AF:
0.425
Gnomad ASJ
AF:
0.252
Gnomad EAS
AF:
0.715
Gnomad SAS
AF:
0.525
Gnomad FIN
AF:
0.385
Gnomad MID
AF:
0.288
Gnomad NFE
AF:
0.283
Gnomad OTH
AF:
0.284
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.284
AC:
43209
AN:
151930
Hom.:
7591
Cov.:
32
AF XY:
0.297
AC XY:
22066
AN XY:
74260
show subpopulations
Gnomad4 AFR
AF:
0.129
Gnomad4 AMR
AF:
0.426
Gnomad4 ASJ
AF:
0.252
Gnomad4 EAS
AF:
0.714
Gnomad4 SAS
AF:
0.523
Gnomad4 FIN
AF:
0.385
Gnomad4 NFE
AF:
0.283
Gnomad4 OTH
AF:
0.286
Alfa
AF:
0.273
Hom.:
3280
Bravo
AF:
0.280
Asia WGS
AF:
0.598
AC:
2075
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
6.7
DANN
Benign
0.83

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: rs1014638; hg19: chr3-39326283; API