chr4-25790562-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_015187.5(SEL1L3):c.1969A>G(p.Thr657Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00069 in 1,608,042 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0037 ( 4 hom., cov: 30)
Exomes 𝑓: 0.00038 ( 3 hom. )
Consequence
SEL1L3
NM_015187.5 missense
NM_015187.5 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 0.766
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0059874356).
BP6
?
Variant 4-25790562-T-C is Benign according to our data. Variant chr4-25790562-T-C is described in ClinVar as [Benign]. Clinvar id is 783419.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEL1L3 | NM_015187.5 | c.1969A>G | p.Thr657Ala | missense_variant | 12/24 | ENST00000399878.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEL1L3 | ENST00000399878.8 | c.1969A>G | p.Thr657Ala | missense_variant | 12/24 | 1 | NM_015187.5 | P1 | |
SEL1L3 | ENST00000264868.9 | c.1864A>G | p.Thr622Ala | missense_variant | 12/24 | 1 | |||
SEL1L3 | ENST00000502949.5 | c.1510A>G | p.Thr504Ala | missense_variant | 12/24 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00373 AC: 562AN: 150752Hom.: 4 Cov.: 30
GnomAD3 genomes
?
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150752
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GnomAD3 exomes AF: 0.000847 AC: 210AN: 247904Hom.: 0 AF XY: 0.000654 AC XY: 88AN XY: 134600
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GnomAD4 exome AF: 0.000375 AC: 547AN: 1457172Hom.: 3 Cov.: 29 AF XY: 0.000321 AC XY: 233AN XY: 725198
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GnomAD4 genome ? AF: 0.00373 AC: 562AN: 150870Hom.: 4 Cov.: 30 AF XY: 0.00368 AC XY: 271AN XY: 73592
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ESP6500AA
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ExAC
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129
Asia WGS
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AN:
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 | Jun 21, 2018 | - - |
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
D
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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