GeneBe

chr10-14618200-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031453.4(FAM107B):​c.469+49434G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,030 control chromosomes in the GnomAD database, including 4,637 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 0.24 ( 4637 hom., cov: 31)

Consequence

FAM107B
NM_031453.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.301

Publications

5 publications found
Variant links:
Genes affected
FAM107B (HGNC:23726): (family with sequence similarity 107 member B) Predicted to act upstream of or within sensory perception of sound. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.88).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM107BNM_031453.4 linkc.469+49434G>A intron_variant Intron 2 of 4 ENST00000181796.7 NP_113641.2 Q9H098-2
FAM107BNM_001282695.2 linkc.-123+49434G>A intron_variant Intron 2 of 5 NP_001269624.1 Q9H098-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM107BENST00000181796.7 linkc.469+49434G>A intron_variant Intron 2 of 4 2 NM_031453.4 ENSP00000181796.2 Q9H098-2
FAM107BENST00000487335.5 linkn.469+49434G>A intron_variant Intron 2 of 5 1 ENSP00000420273.1 F8WDH7

Frequencies

GnomAD3 genomes
AF:
0.242
AC:
36755
AN:
151912
Hom.:
4629
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.236
Gnomad AMI
AF:
0.187
Gnomad AMR
AF:
0.331
Gnomad ASJ
AF:
0.137
Gnomad EAS
AF:
0.167
Gnomad SAS
AF:
0.233
Gnomad FIN
AF:
0.188
Gnomad MID
AF:
0.196
Gnomad NFE
AF:
0.248
Gnomad OTH
AF:
0.212
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.242
AC:
36809
AN:
152030
Hom.:
4637
Cov.:
31
AF XY:
0.240
AC XY:
17825
AN XY:
74322
show subpopulations
African (AFR)
AF:
0.236
AC:
9798
AN:
41454
American (AMR)
AF:
0.331
AC:
5062
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.137
AC:
476
AN:
3468
East Asian (EAS)
AF:
0.167
AC:
865
AN:
5172
South Asian (SAS)
AF:
0.234
AC:
1127
AN:
4816
European-Finnish (FIN)
AF:
0.188
AC:
1983
AN:
10570
Middle Eastern (MID)
AF:
0.187
AC:
55
AN:
294
European-Non Finnish (NFE)
AF:
0.248
AC:
16823
AN:
67962
Other (OTH)
AF:
0.214
AC:
451
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1431
2862
4292
5723
7154
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
380
760
1140
1520
1900
<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:
0.243
Hom.:
10217
Bravo
AF:
0.251
Asia WGS
AF:
0.214
AC:
747
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.8
DANN
Benign
0.52
PhyloP100
-0.30
Mutation Taster
=100/0
polymorphism (auto)

Splicing

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

Publications

Other links and lift over

dbSNP: rs7921651; hg19: chr10-14660199; API