chr11-78064306-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003251.4(THRSP):c.425C>T(p.Thr142Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 1,610,652 control chromosomes in the GnomAD database, including 178 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0086 ( 7 hom., cov: 32)
Exomes 𝑓: 0.013 ( 171 hom. )
Consequence
THRSP
NM_003251.4 missense
NM_003251.4 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 1.68
Genes affected
THRSP (HGNC:11800): (thyroid hormone responsive) The protein encoded by this gene is similar to the gene product of S14, a rat gene whose expression is limited to liver and adipose tissue and is controlled by nutritional and hormonal factors. This gene has been shown to be expressed in liver and adipocytes, particularly in lipomatous modules. It is also found to be expressed in lipogenic breast cancers, which suggests a role in controlling tumor lipid metabolism. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0039934516).
BP6
?
Variant 11-78064306-C-T is Benign according to our data. Variant chr11-78064306-C-T is described in ClinVar as [Benign]. Clinvar id is 771892.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THRSP | NM_003251.4 | c.425C>T | p.Thr142Met | missense_variant | 1/2 | ENST00000281030.2 | |
NDUFC2-KCTD14 | NM_001203262.2 | c.166+15273G>A | intron_variant | ||||
NDUFC2-KCTD14 | NM_001203260.2 | c.310+8692G>A | intron_variant | ||||
NDUFC2-KCTD14 | NM_001203261.2 | c.310+8692G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THRSP | ENST00000281030.2 | c.425C>T | p.Thr142Met | missense_variant | 1/2 | 1 | NM_003251.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00858 AC: 1301AN: 151720Hom.: 7 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.00807 AC: 2004AN: 248190Hom.: 20 AF XY: 0.00814 AC XY: 1092AN XY: 134228
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GnomAD4 exome AF: 0.0126 AC: 18331AN: 1458816Hom.: 171 Cov.: 31 AF XY: 0.0121 AC XY: 8803AN XY: 725604
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GnomAD4 genome ? AF: 0.00857 AC: 1301AN: 151836Hom.: 7 Cov.: 32 AF XY: 0.00819 AC XY: 607AN XY: 74150
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Asia WGS
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
D;D;N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at