rs144179214

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_021822.4(APOBEC3G):​c.1106A>C​(p.Gln369Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,672 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

APOBEC3G
NM_021822.4 missense

Scores

1
3
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0870
Variant links:
Genes affected
APOBEC3G (HGNC:17357): (apolipoprotein B mRNA editing enzyme catalytic subunit 3G) This gene is a member of the cytidine deaminase gene family. It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22. Members of the cluster encode proteins that are structurally and functionally related to the C to U RNA-editing cytidine deaminase APOBEC1. The protein encoded by this gene catalyzes site-specific deamination of both RNA and single-stranded DNA. The encoded protein has been found to be a specific inhibitor of human immunodeficiency virus-1 (HIV-1) infectivity. [provided by RefSeq, Mar 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.40859315).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
APOBEC3GNM_021822.4 linkc.1106A>C p.Gln369Pro missense_variant Exon 7 of 8 ENST00000407997.4 NP_068594.1 Q9HC16-1
APOBEC3GNM_001349436.1 linkc.1073A>C p.Gln358Pro missense_variant Exon 7 of 8 NP_001336365.1
APOBEC3GNM_001349437.2 linkc.905A>C p.Gln302Pro missense_variant Exon 6 of 7 NP_001336366.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
APOBEC3GENST00000407997.4 linkc.1106A>C p.Gln369Pro missense_variant Exon 7 of 8 1 NM_021822.4 ENSP00000385057.3 Q9HC16-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461672
Hom.:
0
Cov.:
32
AF XY:
0.00000138
AC XY:
1
AN XY:
727110
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.31
BayesDel_addAF
Benign
-0.039
T
BayesDel_noAF
Benign
-0.29
CADD
Benign
13
DANN
Benign
0.97
DEOGEN2
Benign
0.085
T
Eigen
Benign
-0.42
Eigen_PC
Benign
-0.73
FATHMM_MKL
Benign
0.011
N
LIST_S2
Uncertain
0.89
D
M_CAP
Benign
0.018
T
MetaRNN
Benign
0.41
T
MetaSVM
Benign
-0.74
T
MutationAssessor
Pathogenic
3.0
M
PROVEAN
Uncertain
-3.5
D
REVEL
Benign
0.20
Sift
Uncertain
0.015
D
Sift4G
Benign
0.076
T
Polyphen
0.85
P
Vest4
0.40
MutPred
0.57
Loss of helix (P = 0.079);
MVP
0.75
MPC
0.71
ClinPred
0.68
D
GERP RS
0.46
Varity_R
0.89
gMVP
0.50

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-39483097; API