Genetic Variant ENST00000752489.1:n.172-3338G>A (chr4-176516966-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000752489.1(ENSG00000298014):n.172-3338G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,056 control chromosomes in the GnomAD database, including 26,140 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 0.59 ( 26140 hom., cov: 29)

Consequence

ENSG00000298014
ENST00000752489.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.256

Publications

3 publications found

Variant links:

Genes affected

ENSG00000298014 (HGNC:):

ENSG00000298014 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900817	XR_007058376.1 link	n.1158-3338G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298014	ENST00000752489.1 link	n.172-3338G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.586

AC:

88448

AN:

150938

Hom.:

26106

Cov.:

show subpopulations

Gnomad AFR

AF:

0.653

Gnomad AMI

AF:

0.377

Gnomad AMR

AF:

0.578

Gnomad ASJ

AF:

0.544

Gnomad EAS

AF:

0.407

Gnomad SAS

AF:

0.590

Gnomad FIN

AF:

0.569

Gnomad MID

AF:

0.564

Gnomad NFE

AF:

0.568

Gnomad OTH

AF:

0.598

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

GnomAD4 genome

AF:

0.586

AC:

88534

AN:

151056

Hom.:

26140

Cov.:

AF XY:

0.585

AC XY:

43163

AN XY:

73744

show subpopulations

African (AFR)

AF:

0.653

AC:

26840

AN:

41104

American (AMR)

AF:

0.578

AC:

8782

AN:

15206

Ashkenazi Jewish (ASJ)

AF:

0.544

AC:

1885

AN:

3468

East Asian (EAS)

AF:

0.407

AC:

2086

AN:

5124

South Asian (SAS)

AF:

0.591

AC:

2828

AN:

4788

European-Finnish (FIN)

AF:

0.569

AC:

5852

AN:

10278

Middle Eastern (MID)

AF:

0.575

AC:

168

AN:

292

European-Non Finnish (NFE)

AF:

0.568

AC:

38497

AN:

67784

Other (OTH)

AF:

0.596

AC:

1253

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

1711

3422

5132

6843

8554

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

748

1496

2244

2992

3740

<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:

0.603

Hom.:

4815

Bravo

AF:

0.584

Asia WGS

AF:

0.507

AC:

1759

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.20

(source)

DANN

Benign

0.44

PhyloP100

-0.26

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