rs911602
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020641.3(EQTN):c.421+292T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,152 control chromosomes in the GnomAD database, including 21,372 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 0.51 ( 21372 hom., cov: 34)
Consequence
EQTN
NM_020641.3 intron
NM_020641.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.752
Genes affected
EQTN (HGNC:1359): (equatorin) Predicted to be involved in acrosomal vesicle exocytosis; endocytosis; and fusion of sperm to egg plasma membrane involved in single fertilization. Predicted to be located in acrosomal membrane; early endosome; and nucleus. Predicted to be active in inner acrosomal membrane; outer acrosomal membrane; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EQTN | NM_020641.3 | c.421+292T>G | intron_variant | ENST00000380032.8 | |||
EQTN | NM_001161585.2 | c.334+292T>G | intron_variant | ||||
EQTN | XM_011517920.2 | c.13+292T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EQTN | ENST00000380032.8 | c.421+292T>G | intron_variant | 1 | NM_020641.3 | P1 | |||
EQTN | ENST00000537675.5 | c.334+292T>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.513 AC: 78002AN: 152034Hom.: 21358 Cov.: 34
GnomAD3 genomes
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34
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.513 AC: 78048AN: 152152Hom.: 21372 Cov.: 34 AF XY: 0.512 AC XY: 38103AN XY: 74374
GnomAD4 genome
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38103
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74374
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1832
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3472
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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