chr1-183647821-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_203454.3(APOBEC4):c.961A>G(p.Asn321Asp) variant causes a missense change. The variant allele was found at a frequency of 0.00244 in 1,614,220 control chromosomes in the GnomAD database, including 95 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 49 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 46 hom. )
Consequence
APOBEC4
NM_203454.3 missense
NM_203454.3 missense
Scores
1
5
12
Clinical Significance
Conservation
PhyloP100: 5.36
Genes affected
APOBEC4 (HGNC:32152): (apolipoprotein B mRNA editing enzyme catalytic polypeptide like 4) This gene encodes a member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases, which convert cytidine to uridine. Other AID/APOBEC family members are involved in mRNA editing, somatic hypermutation and recombination of immunoglobulin genes, and innate immunity to retroviral infection. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.003106892).
BP6
?
Variant 1-183647821-T-C is Benign according to our data. Variant chr1-183647821-T-C is described in ClinVar as [Benign]. Clinvar id is 783956.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.013 (1983/152330) while in subpopulation AFR AF= 0.0457 (1900/41568). AF 95% confidence interval is 0.044. There are 49 homozygotes in gnomad4. There are 913 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 48 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOBEC4 | NM_203454.3 | c.961A>G | p.Asn321Asp | missense_variant | 2/2 | ENST00000308641.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOBEC4 | ENST00000308641.6 | c.961A>G | p.Asn321Asp | missense_variant | 2/2 | 1 | NM_203454.3 | P1 | |
RGL1 | ENST00000304685.8 | c.-33+11320T>C | intron_variant | 1 | |||||
APOBEC4 | ENST00000481562.1 | n.246-24A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0130 AC: 1979AN: 152212Hom.: 48 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1979
AN:
152212
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00331 AC: 832AN: 251482Hom.: 14 AF XY: 0.00258 AC XY: 350AN XY: 135914
GnomAD3 exomes
AF:
AC:
832
AN:
251482
Hom.:
AF XY:
AC XY:
350
AN XY:
135914
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00134 AC: 1960AN: 1461890Hom.: 46 Cov.: 66 AF XY: 0.00113 AC XY: 821AN XY: 727246
GnomAD4 exome
AF:
AC:
1960
AN:
1461890
Hom.:
Cov.:
66
AF XY:
AC XY:
821
AN XY:
727246
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0130 AC: 1983AN: 152330Hom.: 49 Cov.: 32 AF XY: 0.0123 AC XY: 913AN XY: 74498
GnomAD4 genome
?
AF:
AC:
1983
AN:
152330
Hom.:
Cov.:
32
AF XY:
AC XY:
913
AN XY:
74498
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ESP6500AA
AF:
AC:
212
ESP6500EA
AF:
AC:
0
ExAC
?
AF:
AC:
503
Asia WGS
AF:
AC:
5
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at