8-8027948-C-G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001423531.1(FAM90A12):c.1083G>C(p.Arg361Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000257 in 116,564 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 24)
Exomes 𝑓: 0.00018 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
FAM90A12
NM_001423531.1 synonymous
NM_001423531.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.688
Publications
0 publications found
Genes affected
FAM90A12 (HGNC:32260): (family with sequence similarity 90 member A12) FAM90A12 belongs to subfamily II of the primate-specific FAM90A gene family, which originated from multiple duplications and rearrangements (Bosch et al., 2007 [PubMed 17684299]). For background information on the FAM90A gene family, as well as information on the evolution of FAM90A genes, see FAM90A1 (MIM 613041).[supplied by OMIM, Jul 2010]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 8-8027948-C-G is Benign according to our data. Variant chr8-8027948-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 3771062.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.688 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001423531.1. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes 0.0000257 AC: 3AN: 116526Hom.: 0 Cov.: 24 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
116526
Hom.:
Cov.:
24
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:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000180 AC: 135AN: 750822Hom.: 1 Cov.: 10 AF XY: 0.000156 AC XY: 61AN XY: 391684 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
135
AN:
750822
Hom.:
Cov.:
10
AF XY:
AC XY:
61
AN XY:
391684
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
21804
American (AMR)
AF:
AC:
14
AN:
30898
Ashkenazi Jewish (ASJ)
AF:
AC:
3
AN:
19800
East Asian (EAS)
AF:
AC:
13
AN:
29568
South Asian (SAS)
AF:
AC:
8
AN:
62222
European-Finnish (FIN)
AF:
AC:
8
AN:
32346
Middle Eastern (MID)
AF:
AC:
0
AN:
2784
European-Non Finnish (NFE)
AF:
AC:
84
AN:
515388
Other (OTH)
AF:
AC:
5
AN:
36012
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.274
Heterozygous variant carriers
0
15
30
44
59
74
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.0000257 AC: 3AN: 116564Hom.: 0 Cov.: 24 AF XY: 0.0000358 AC XY: 2AN XY: 55880 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
3
AN:
116564
Hom.:
Cov.:
24
AF XY:
AC XY:
2
AN XY:
55880
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
35126
American (AMR)
AF:
AC:
1
AN:
10236
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2792
East Asian (EAS)
AF:
AC:
0
AN:
3128
South Asian (SAS)
AF:
AC:
0
AN:
3204
European-Finnish (FIN)
AF:
AC:
0
AN:
6970
Middle Eastern (MID)
AF:
AC:
0
AN:
248
European-Non Finnish (NFE)
AF:
AC:
2
AN:
52568
Other (OTH)
AF:
AC:
0
AN:
1630
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.258
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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