chr3-24185684-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001354712.2(THRB):c.283+4390C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,898 control chromosomes in the GnomAD database, including 11,153 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 0.37 ( 11153 hom., cov: 31)
Consequence
THRB
NM_001354712.2 intron
NM_001354712.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.190
Publications
3 publications found
Genes affected
THRB (HGNC:11799): (thyroid hormone receptor beta) The protein encoded by this gene is a nuclear hormone receptor for triiodothyronine. It is one of the several receptors for thyroid hormone, and has been shown to mediate the biological activities of thyroid hormone. Knockout studies in mice suggest that the different receptors, while having certain extent of redundancy, may mediate different functions of thyroid hormone. Mutations in this gene are known to be a cause of generalized thyroid hormone resistance (GTHR), a syndrome characterized by goiter and high levels of circulating thyroid hormone (T3-T4), with normal or slightly elevated thyroid stimulating hormone (TSH). Several alternatively spliced transcript variants encoding the same protein have been observed for this gene. [provided by RefSeq, Jul 2008]
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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=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
THRB | NM_001354712.2 | c.283+4390C>T | intron_variant | Intron 5 of 10 | ENST00000646209.2 | NP_001341641.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.374 AC: 56786AN: 151780Hom.: 11148 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
56786
AN:
151780
Hom.:
Cov.:
31
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: 0.374 AC: 56820AN: 151898Hom.: 11153 Cov.: 31 AF XY: 0.374 AC XY: 27766AN XY: 74244 show subpopulations
GnomAD4 genome
AF:
AC:
56820
AN:
151898
Hom.:
Cov.:
31
AF XY:
AC XY:
27766
AN XY:
74244
show subpopulations
African (AFR)
AF:
AC:
20572
AN:
41384
American (AMR)
AF:
AC:
5120
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
AC:
1095
AN:
3466
East Asian (EAS)
AF:
AC:
1077
AN:
5160
South Asian (SAS)
AF:
AC:
1826
AN:
4812
European-Finnish (FIN)
AF:
AC:
3511
AN:
10552
Middle Eastern (MID)
AF:
AC:
96
AN:
294
European-Non Finnish (NFE)
AF:
AC:
22537
AN:
67952
Other (OTH)
AF:
AC:
768
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1777
3554
5330
7107
8884
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
542
1084
1626
2168
2710
<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:
998
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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