rs1861972
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001427.4(EN2):c.686-1073G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,216 control chromosomes in the GnomAD database, including 40,444 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.73 ( 40444 hom., cov: 35)
Consequence
EN2
NM_001427.4 intron
NM_001427.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.40
Genes affected
EN2 (HGNC:3343): (engrailed homeobox 2) Homeobox-containing genes are thought to have a role in controlling development. In Drosophila, the 'engrailed' (en) gene plays an important role during development in segmentation, where it is required for the formation of posterior compartments. Different mutations in the mouse homologs, En1 and En2, produced different developmental defects that frequently are lethal. The human engrailed homologs 1 and 2 encode homeodomain-containing proteins and have been implicated in the control of pattern formation during development of the central nervous system. [provided by RefSeq, Jul 2008]
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EN2 | NM_001427.4 | c.686-1073G>A | intron_variant | ENST00000297375.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EN2 | ENST00000297375.4 | c.686-1073G>A | intron_variant | 1 | NM_001427.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.727 AC: 110569AN: 152098Hom.: 40386 Cov.: 35
GnomAD3 genomes
?
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110569
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152098
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35
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.727 AC: 110688AN: 152216Hom.: 40444 Cov.: 35 AF XY: 0.725 AC XY: 53967AN XY: 74406
GnomAD4 genome
?
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110688
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152216
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35
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53967
AN XY:
74406
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Asia WGS
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2793
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3478
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Autism, susceptibility to, 10 Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Nov 01, 2005 | - - |
Computational scores
Source:
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