7-155461298-G-A

Variant names:

• chr7-155461298-G-A
• rs1861972
• NM_001427.4:c.686-1073G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: -1.40
• Publications: 30 publications found

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]

EN2 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001427.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EN2	NM_001427.4	MANE Select	c.686-1073G>A		intron	N/A	NP_001418.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EN2	ENST00000297375.4	TSL:1 MANE Select	c.686-1073G>A		intron	N/A	ENSP00000297375.4

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110569 AN: 152098 Hom.: 40386 Cov.: 35

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.731

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.727 AC: 110688 AN: 152216 Hom.: 40444 Cov.: 35 AF XY: 0.725 AC XY: 53967 AN XY: 74406

African (AFR) AF: 0.731 AC: 30337 AN: 41528

American (AMR) AF: 0.782 AC: 11966 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2422 AN: 3472

East Asian (EAS) AF: 0.939 AC: 4857 AN: 5172

South Asian (SAS) AF: 0.688 AC: 3316 AN: 4820

European-Finnish (FIN) AF: 0.672 AC: 7117 AN: 10598

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48336 AN: 68004

Other (OTH) AF: 0.731 AC: 1543 AN: 2110

Alfa AF: 0.683 Hom.: 5329

Bravo AF: 0.740

Asia WGS AF: 0.804 AC: 2793 AN: 3478

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Autism, susceptibility to, 10 Uncertain:1

Nov 01, 2005

OMIM

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: literature only

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.047
DANN	Benign	0.44
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1861972; hg19: chr7-155253993;