rs79069095
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_001077706.3(ECT2L):c.1579-1G>A variant causes a splice acceptor change. The variant allele was found at a frequency of 0.000000687 in 1,455,984 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/2 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
ECT2L
NM_001077706.3 splice_acceptor
NM_001077706.3 splice_acceptor
Scores
1
4
2
Splicing: ADA: 0.9999
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.78
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PVS1
?
Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.031675875 fraction of the gene. Cryptic splice site detected, with MaxEntScore 3.4, offset of 1, new splice context is: gtttccattcaatcttcaAGaaa. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ECT2L | NM_001077706.3 | c.1579-1G>A | splice_acceptor_variant | ENST00000541398.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ECT2L | ENST00000541398.7 | c.1579-1G>A | splice_acceptor_variant | 5 | NM_001077706.3 | P1 | |||
ECT2L | ENST00000367682.6 | c.1579-1G>A | splice_acceptor_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 247898Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134518
GnomAD3 exomes
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GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455984Hom.: 0 Cov.: 27 AF XY: 0.00000138 AC XY: 1AN XY: 724552
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ExAC
?
AF:
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1
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
D;D;D
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at