Genetic Variant ENSG00000251199:n.382-61998A>G (chr4-134228646-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000654404.1(ENSG00000251199):n.382-61998A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,860 control chromosomes in the GnomAD database, including 14,651 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 0.41 ( 14651 hom., cov: 32)

Consequence

ENSG00000251199
ENST00000654404.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.552

Publications

3 publications found

Variant links:

Genes affected

ENSG00000251199 (HGNC:):

ENSG00000251199 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000251199	ENST00000654404.1 link	n.382-61998A>G	intron_variant	Intron 2 of 7
ENSG00000251199	ENST00000658033.2 link	n.415-61998A>G	intron_variant	Intron 2 of 4
ENSG00000251199	ENST00000658435.1 link	n.411+78895A>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.411

AC:

62358

AN:

151744

Hom.:

14638

Cov.:

show subpopulations

Gnomad AFR

AF:

0.561

Gnomad AMI

AF:

0.354

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.352

Gnomad EAS

AF:

0.970

Gnomad SAS

AF:

0.417

Gnomad FIN

AF:

0.353

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.285

Gnomad OTH

AF:

0.384

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

GnomAD4 genome

AF:

0.411

AC:

62407

AN:

151860

Hom.:

14651

Cov.:

AF XY:

0.418

AC XY:

30987

AN XY:

74214

show subpopulations

African (AFR)

AF:

0.560

AC:

23198

AN:

41390

American (AMR)

AF:

0.439

AC:

6692

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.352

AC:

1222

AN:

3468

East Asian (EAS)

AF:

0.970

AC:

5017

AN:

5170

South Asian (SAS)

AF:

0.416

AC:

2000

AN:

4812

European-Finnish (FIN)

AF:

0.353

AC:

3711

AN:

10526

Middle Eastern (MID)

AF:

0.312

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.285

AC:

19332

AN:

67932

Other (OTH)

AF:

0.389

AC:

821

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1692

3384

5075

6767

8459

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

570

1140

1710

2280

2850

<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:

0.334

Hom.:

36633

Bravo

AF:

0.427

Asia WGS

AF:

0.668

AC:

2305

AN:

3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

5.1

(source)

DANN

Benign

0.59

PhyloP100

0.55

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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