NM_198215.4:c.325-7126A>T

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0110

Publications

0 publications found
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM13CNM_198215.4 linkc.325-7126A>T intron_variant Intron 3 of 13 ENST00000618804.5 NP_937858.2 Q8NE31-1A8K181

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM13CENST00000618804.5 linkc.325-7126A>T intron_variant Intron 3 of 13 1 NM_198215.4 ENSP00000481854.1 Q8NE31-1

Frequencies

GnomAD3 genomes
AF:
0.450
AC:
68274
AN:
151872
Hom.:
16281
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.618
Gnomad AMI
AF:
0.386
Gnomad AMR
AF:
0.399
Gnomad ASJ
AF:
0.376
Gnomad EAS
AF:
0.494
Gnomad SAS
AF:
0.475
Gnomad FIN
AF:
0.357
Gnomad MID
AF:
0.380
Gnomad NFE
AF:
0.373
Gnomad OTH
AF:
0.427
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.450
AC:
68342
AN:
151990
Hom.:
16305
Cov.:
32
AF XY:
0.448
AC XY:
33273
AN XY:
74288
show subpopulations
African (AFR)
AF:
0.618
AC:
25599
AN:
41434
American (AMR)
AF:
0.399
AC:
6090
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.376
AC:
1304
AN:
3470
East Asian (EAS)
AF:
0.494
AC:
2546
AN:
5158
South Asian (SAS)
AF:
0.476
AC:
2289
AN:
4812
European-Finnish (FIN)
AF:
0.357
AC:
3773
AN:
10560
Middle Eastern (MID)
AF:
0.361
AC:
106
AN:
294
European-Non Finnish (NFE)
AF:
0.374
AC:
25385
AN:
67964
Other (OTH)
AF:
0.426
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:
0.253
Hom.:
557
Bravo
AF:
0.460
Asia WGS
AF:
0.501
AC:
1738
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.2
DANN
Benign
0.44
PhyloP100
-0.011
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs166924; hg19: chr10-61090992; API