Genetic Variant ENST00000720028.1:n.90+13253G>A (chr2-105722228-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000720028.1(ENSG00000293937):n.90+13253G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,118 control chromosomes in the GnomAD database, including 5,438 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 ( 5438 hom., cov: 32)

Consequence

ENSG00000293937
ENST00000720028.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.941

Publications

7 publications found

Variant links:

Genes affected

ENSG00000293937 (HGNC:):

ENSG00000293937 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 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
ENSG00000293937	ENST00000720028.1 link	n.90+13253G>A		intron_variant	Intron 1 of 1
ENSG00000293937	ENST00000720029.1 link	n.259+11932G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.251

AC:

38129

AN:

152000

Hom.:

5436

Cov.:

show subpopulations

Gnomad AFR

AF:

0.120

Gnomad AMI

AF:

0.361

Gnomad AMR

AF:

0.243

Gnomad ASJ

AF:

0.299

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.254

Gnomad FIN

AF:

0.348

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.322

Gnomad OTH

AF:

0.245

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

GnomAD4 genome

AF:

0.251

AC:

38137

AN:

152118

Hom.:

5438

Cov.:

AF XY:

0.251

AC XY:

18671

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.120

AC:

4985

AN:

41524

American (AMR)

AF:

0.243

AC:

3716

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.299

AC:

1037

AN:

3472

East Asian (EAS)

AF:

0.134

AC:

692

AN:

5170

South Asian (SAS)

AF:

0.255

AC:

1229

AN:

4816

European-Finnish (FIN)

AF:

0.348

AC:

3681

AN:

10570

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.322

AC:

21873

AN:

67978

Other (OTH)

AF:

0.242

AC:

510

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1429

2857

4286

5714

7143

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

394

788

1182

1576

1970

<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:

0.298

Hom.:

9801

Bravo

AF:

0.240

Asia WGS

AF:

0.182

AC:

630

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.6

(source)

DANN

Benign

0.85

PhyloP100

0.94

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