Genetic Variant ENST00000755294.1:n.190+3610C>T (chr4-117780291-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 ENST00000755294.1(ENSG00000288921):n.190+3610C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,762 control chromosomes in the GnomAD database, including 25,162 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 0.55 ( 25162 hom., cov: 32)

Consequence

ENSG00000288921
ENST00000755294.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.306

Publications

8 publications found

Variant links:

Genes affected

ENSG00000288921 (HGNC:):

ENSG00000288921 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000288921	ENST00000755294.1 link	n.190+3610C>T	intron_variant	Intron 2 of 5
ENSG00000288921	ENST00000755295.1 link	n.166+3610C>T	intron_variant	Intron 2 of 3
ENSG00000288921	ENST00000755296.1 link	n.156+3610C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.552

AC:

83660

AN:

151644

Hom.:

25114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.806

Gnomad AMI

AF:

0.613

Gnomad AMR

AF:

0.546

Gnomad ASJ

AF:

0.489

Gnomad EAS

AF:

0.608

Gnomad SAS

AF:

0.416

Gnomad FIN

AF:

0.416

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.426

Gnomad OTH

AF:

0.555

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

GnomAD4 genome

AF:

0.552

AC:

83770

AN:

151762

Hom.:

25162

Cov.:

AF XY:

0.551

AC XY:

40857

AN XY:

74162

show subpopulations

African (AFR)

AF:

0.807

AC:

33448

AN:

41470

American (AMR)

AF:

0.546

AC:

8289

AN:

15190

Ashkenazi Jewish (ASJ)

AF:

0.489

AC:

1694

AN:

3464

East Asian (EAS)

AF:

0.607

AC:

3129

AN:

5154

South Asian (SAS)

AF:

0.418

AC:

2015

AN:

4824

European-Finnish (FIN)

AF:

0.416

AC:

4384

AN:

10526

Middle Eastern (MID)

AF:

0.643

AC:

189

AN:

294

European-Non Finnish (NFE)

AF:

0.426

AC:

28894

AN:

67826

Other (OTH)

AF:

0.556

AC:

1170

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1738

3475

5213

6950

8688

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

680

1360

2040

2720

3400

<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:

0.468

Hom.:

4994

Bravo

AF:

0.580

Asia WGS

AF:

0.508

AC:

1759

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

6.1

(source)

DANN

Benign

0.69

PhyloP100

0.31

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