rs77871185
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_017709.4(TENT5C):āc.841A>Gā(p.Ile281Val) variant causes a missense change. The variant allele was found at a frequency of 0.00354 in 1,614,162 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: š 0.0026 ( 2 hom., cov: 31)
Exomes š: 0.0036 ( 14 hom. )
Consequence
TENT5C
NM_017709.4 missense
NM_017709.4 missense
Scores
3
15
Clinical Significance
Conservation
PhyloP100: 7.02
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.006962985).
BS2
?
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENT5C | NM_017709.4 | c.841A>G | p.Ile281Val | missense_variant | 2/2 | ENST00000369448.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENT5C | ENST00000369448.4 | c.841A>G | p.Ile281Val | missense_variant | 2/2 | 1 | NM_017709.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00260 AC: 396AN: 152168Hom.: 2 Cov.: 31
GnomAD3 genomes
?
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396
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152168
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31
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GnomAD3 exomes AF: 0.00257 AC: 644AN: 250998Hom.: 3 AF XY: 0.00255 AC XY: 346AN XY: 135694
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GnomAD4 exome AF: 0.00363 AC: 5311AN: 1461876Hom.: 14 Cov.: 35 AF XY: 0.00358 AC XY: 2605AN XY: 727242
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GnomAD4 genome ? AF: 0.00260 AC: 396AN: 152286Hom.: 2 Cov.: 31 AF XY: 0.00235 AC XY: 175AN XY: 74468
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ESP6500AA
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35
ExAC
?
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325
Asia WGS
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3478
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
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
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Uncertain
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