Genetic Variant ENST00000419225.1:n.110+973_110+974insGC (chr7-155456016-A-AGC) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000419225.1(EN2-DT):n.110+973_110+974insGC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.49 ( 19443 hom., cov: 0)

Consequence

EN2-DT
ENST00000419225.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.561

Publications

1 publications found

Variant links:

Genes affected

EN2-DT (HGNC:55659): (EN2 divergent transcript)

EN2-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EN2-DT	NR_186580.1 link	n.129+972_129+973dupGC		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
EN2-DT	ENST00000419225.1 link	n.110+973_110+974insGC	intron_variant	Intron 1 of 2	4
EN2-DT	ENST00000781270.1 link	n.107+973_107+974insGC	intron_variant	Intron 1 of 4
EN2-DT	ENST00000781271.1 link	n.86+973_86+974insGC	intron_variant	Intron 1 of 4
EN2-DT	ENST00000781273.1 link	n.130+973_130+974insGC	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.494

AC:

74901

AN:

151610

Hom.:

19425

Cov.:

show subpopulations

Gnomad AFR

AF:

0.629

Gnomad AMI

AF:

0.339

Gnomad AMR

AF:

0.446

Gnomad ASJ

AF:

0.378

Gnomad EAS

AF:

0.810

Gnomad SAS

AF:

0.585

Gnomad FIN

AF:

0.400

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.417

Gnomad OTH

AF:

0.468

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

GnomAD4 genome

AF:

0.494

AC:

74958

AN:

151728

Hom.:

19443

Cov.:

AF XY:

0.498

AC XY:

36896

AN XY:

74150

show subpopulations

African (AFR)

AF:

0.628

AC:

25931

AN:

41270

American (AMR)

AF:

0.445

AC:

6799

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.378

AC:

1312

AN:

3470

East Asian (EAS)

AF:

0.810

AC:

4160

AN:

5134

South Asian (SAS)

AF:

0.585

AC:

2820

AN:

4824

European-Finnish (FIN)

AF:

0.400

AC:

4215

AN:

10542

Middle Eastern (MID)

AF:

0.377

AC:

110

AN:

292

European-Non Finnish (NFE)

AF:

0.417

AC:

28318

AN:

67924

Other (OTH)

AF:

0.469

AC:

985

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1879

3758

5638

7517

9396

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

666

1332

1998

2664

3330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.460

Hom.:

1740

Bravo

AF:

0.497

Asia WGS

AF:

0.655

AC:

2279

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.56

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over