rs1054735
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006288.5(THY1):c.*84C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000654 in 1,225,090 control chromosomes in the GnomAD database, including 5 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 0.0031 ( 3 hom., cov: 31)
Exomes 𝑓: 0.00031 ( 2 hom. )
Consequence
THY1
NM_006288.5 3_prime_UTR
NM_006288.5 3_prime_UTR
Scores
1
13
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00700
Genes affected
THY1 (HGNC:11801): (Thy-1 cell surface antigen) This gene encodes a cell surface glycoprotein and member of the immunoglobulin superfamily of proteins. The encoded protein is involved in cell adhesion and cell communication in numerous cell types, but particularly in cells of the immune and nervous systems. The encoded protein is widely used as a marker for hematopoietic stem cells. This gene may function as a tumor suppressor in nasopharyngeal carcinoma. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0036794245).
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00305 AC: 464AN: 151888Hom.: 3 Cov.: 31
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GnomAD3 exomes AF: 0.000575 AC: 95AN: 165350Hom.: 0 AF XY: 0.000465 AC XY: 41AN XY: 88118
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GnomAD4 exome AF: 0.000314 AC: 337AN: 1073084Hom.: 2 Cov.: 14 AF XY: 0.000252 AC XY: 137AN XY: 544438
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GnomAD4 genome AF: 0.00305 AC: 464AN: 152006Hom.: 3 Cov.: 31 AF XY: 0.00292 AC XY: 217AN XY: 74306
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
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
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
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ClinPred
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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