NM_001080532.3:c.2459+336C>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001080532.3(TMC3):c.2459+336C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,086 control chromosomes in the GnomAD database, including 6,027 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 0.21 ( 6027 hom., cov: 32)
Consequence
TMC3
NM_001080532.3 intron
NM_001080532.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.00200
Publications
8 publications found
Genes affected
TMC3 (HGNC:22995): (transmembrane channel like 3) Predicted to enable mechanosensitive ion channel activity. Predicted to be involved in ion transmembrane transport. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.213 AC: 32370AN: 151968Hom.: 6009 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
32370
AN:
151968
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: 0.213 AC: 32434AN: 152086Hom.: 6027 Cov.: 32 AF XY: 0.209 AC XY: 15529AN XY: 74376 show subpopulations
GnomAD4 genome
AF:
AC:
32434
AN:
152086
Hom.:
Cov.:
32
AF XY:
AC XY:
15529
AN XY:
74376
show subpopulations
African (AFR)
AF:
AC:
21088
AN:
41438
American (AMR)
AF:
AC:
1681
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
429
AN:
3470
East Asian (EAS)
AF:
AC:
1304
AN:
5162
South Asian (SAS)
AF:
AC:
566
AN:
4814
European-Finnish (FIN)
AF:
AC:
732
AN:
10604
Middle Eastern (MID)
AF:
AC:
49
AN:
294
European-Non Finnish (NFE)
AF:
AC:
6049
AN:
67996
Other (OTH)
AF:
AC:
415
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1019
2039
3058
4078
5097
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
298
596
894
1192
1490
<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:
676
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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