chr10-47305642-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004962.5(GDF10):c.320-4154T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,156 control chromosomes in the GnomAD database, including 1,316 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 0.12 ( 1316 hom., cov: 32)
Consequence
GDF10
NM_004962.5 intron
NM_004962.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0590
Publications
5 publications found
Genes affected
GDF10 (HGNC:4215): (growth differentiation factor 10) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer. This promotes neural repair after stroke. Additionally, this protein may act as a tumor suppressor and reduced expression of this gene is associated with oral cancer. [provided by RefSeq, Jul 2016]
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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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.119 AC: 18128AN: 152040Hom.: 1316 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
18128
AN:
152040
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: 0.119 AC: 18128AN: 152156Hom.: 1316 Cov.: 32 AF XY: 0.119 AC XY: 8883AN XY: 74400 show subpopulations
GnomAD4 genome
AF:
AC:
18128
AN:
152156
Hom.:
Cov.:
32
AF XY:
AC XY:
8883
AN XY:
74400
show subpopulations
African (AFR)
AF:
AC:
1744
AN:
41526
American (AMR)
AF:
AC:
1529
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
AC:
478
AN:
3466
East Asian (EAS)
AF:
AC:
189
AN:
5162
South Asian (SAS)
AF:
AC:
721
AN:
4812
European-Finnish (FIN)
AF:
AC:
1761
AN:
10594
Middle Eastern (MID)
AF:
AC:
42
AN:
292
European-Non Finnish (NFE)
AF:
AC:
11317
AN:
67986
Other (OTH)
AF:
AC:
276
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
834
1669
2503
3338
4172
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
218
436
654
872
1090
<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:
403
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
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