Genetic Variant ENSG00000253690:n.230+28963G>T (chr8-28310063-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000521731.1(ENSG00000253690):n.230+28963G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,912 control chromosomes in the GnomAD database, including 5,398 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 0.25 ( 5398 hom., cov: 32)

Consequence

ENSG00000253690
ENST00000521731.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.641

Publications

7 publications found

Variant links:

Genes affected

ENSG00000253690 (HGNC:):

ENSG00000253690 links:

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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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253690	ENST00000521731.1 link	n.230+28963G>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37354

AN:

151796

Hom.:

5398

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0959

Gnomad AMI

AF:

0.325

Gnomad AMR

AF:

0.344

Gnomad ASJ

AF:

0.313

Gnomad EAS

AF:

0.429

Gnomad SAS

AF:

0.304

Gnomad FIN

AF:

0.233

Gnomad MID

AF:

0.369

Gnomad NFE

AF:

0.294

Gnomad OTH

AF:

0.267

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

GnomAD4 genome

AF:

0.246

AC:

37358

AN:

151912

Hom.:

5398

Cov.:

AF XY:

0.247

AC XY:

18350

AN XY:

74222

show subpopulations

African (AFR)

AF:

0.0957

AC:

3969

AN:

41452

American (AMR)

AF:

0.344

AC:

5248

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.313

AC:

1086

AN:

3472

East Asian (EAS)

AF:

0.429

AC:

2207

AN:

5150

South Asian (SAS)

AF:

0.304

AC:

1459

AN:

4804

European-Finnish (FIN)

AF:

0.233

AC:

2442

AN:

10500

Middle Eastern (MID)

AF:

0.359

AC:

104

AN:

290

European-Non Finnish (NFE)

AF:

0.294

AC:

19970

AN:

67976

Other (OTH)

AF:

0.273

AC:

577

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1338

2676

4015

5353

6691

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

396

792

1188

1584

1980

<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:

0.278

Hom.:

10186

Bravo

AF:

0.248

Asia WGS

AF:

0.372

AC:

1291

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.75

(source)

DANN

Benign

0.69

PhyloP100

-0.64

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