rs144150484
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001077706.3(ECT2L):c.2191C>T(p.His731Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000746 in 1,614,152 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: 𝑓 0.0039 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00042 ( 8 hom. )
Consequence
ECT2L
NM_001077706.3 missense
NM_001077706.3 missense
Scores
3
9
5
Clinical Significance
Conservation
PhyloP100: 5.96
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
?
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ECT2L | NM_001077706.3 | c.2191C>T | p.His731Tyr | missense_variant | 18/22 | ENST00000541398.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ECT2L | ENST00000541398.7 | c.2191C>T | p.His731Tyr | missense_variant | 18/22 | 5 | NM_001077706.3 | P1 | |
ECT2L | ENST00000367682.6 | c.2191C>T | p.His731Tyr | missense_variant | 17/21 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00387 AC: 589AN: 152180Hom.: 3 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.000927 AC: 231AN: 249220Hom.: 1 AF XY: 0.000754 AC XY: 102AN XY: 135210
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GnomAD4 exome AF: 0.000421 AC: 615AN: 1461854Hom.: 8 Cov.: 31 AF XY: 0.000362 AC XY: 263AN XY: 727226
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GnomAD4 genome ? AF: 0.00387 AC: 589AN: 152298Hom.: 3 Cov.: 32 AF XY: 0.00372 AC XY: 277AN XY: 74468
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ExAC
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137
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
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
M;M;M
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;.
REVEL
Uncertain
Sift
Pathogenic
D;D;.
Sift4G
Pathogenic
D;D;D
Polyphen
D;D;D
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
DS_DG_spliceai
Position offset: -2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at