NM_198215.4:c.325-7126A>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_198215.4(FAM13C):c.325-7126A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,990 control chromosomes in the GnomAD database, including 16,305 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 0.45 ( 16305 hom., cov: 32)
Consequence
FAM13C
NM_198215.4 intron
NM_198215.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0110
Publications
0 publications found
Genes affected
FAM13C (HGNC:19371): (family with sequence similarity 13 member C)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.450 AC: 68274AN: 151872Hom.: 16281 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
68274
AN:
151872
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.450 AC: 68342AN: 151990Hom.: 16305 Cov.: 32 AF XY: 0.448 AC XY: 33273AN XY: 74288 show subpopulations
GnomAD4 genome
AF:
AC:
68342
AN:
151990
Hom.:
Cov.:
32
AF XY:
AC XY:
33273
AN XY:
74288
show subpopulations
African (AFR)
AF:
AC:
25599
AN:
41434
American (AMR)
AF:
AC:
6090
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
1304
AN:
3470
East Asian (EAS)
AF:
AC:
2546
AN:
5158
South Asian (SAS)
AF:
AC:
2289
AN:
4812
European-Finnish (FIN)
AF:
AC:
3773
AN:
10560
Middle Eastern (MID)
AF:
AC:
106
AN:
294
European-Non Finnish (NFE)
AF:
AC:
25385
AN:
67964
Other (OTH)
AF:
AC:
899
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1862
3724
5587
7449
9311
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
634
1268
1902
2536
3170
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1738
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.