Genetic Variant ENST00000425894.2:n.292-8129C>T (chr3-5735535-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 ENST00000425894.2(ENSG00000229642):n.292-8129C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 151,850 control chromosomes in the GnomAD database, including 1,553 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 0.11 ( 1553 hom., cov: 32)

Consequence

ENSG00000229642
ENST00000425894.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.720

Publications

2 publications found

Variant links:

Genes affected

ENSG00000229642 (HGNC:):

ENSG00000229642 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000229642	ENST00000425894.2 link	n.292-8129C>T	intron_variant	Intron 2 of 8	3
ENSG00000229642	ENST00000779001.1 link	n.212+39049C>T	intron_variant	Intron 2 of 7
ENSG00000229642	ENST00000779002.1 link	n.232+39049C>T	intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes

AF:

0.111

AC:

16882

AN:

151732

Hom.:

1546

Cov.:

show subpopulations

Gnomad AFR

AF:

0.247

Gnomad AMI

AF:

0.0762

Gnomad AMR

AF:

0.0983

Gnomad ASJ

AF:

0.0467

Gnomad EAS

AF:

0.178

Gnomad SAS

AF:

0.0339

Gnomad FIN

AF:

0.0537

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0446

Gnomad OTH

AF:

0.109

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

GnomAD4 genome

AF:

0.111

AC:

16915

AN:

151850

Hom.:

1553

Cov.:

AF XY:

0.110

AC XY:

8165

AN XY:

74218

show subpopulations

African (AFR)

AF:

0.247

AC:

10240

AN:

41400

American (AMR)

AF:

0.0985

AC:

1502

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.0467

AC:

162

AN:

3470

East Asian (EAS)

AF:

0.178

AC:

914

AN:

5142

South Asian (SAS)

AF:

0.0335

AC:

161

AN:

4804

European-Finnish (FIN)

AF:

0.0537

AC:

566

AN:

10540

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0446

AC:

3032

AN:

67926

Other (OTH)

AF:

0.111

AC:

235

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

680

1361

2041

2722

3402

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

178

356

534

712

890

<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:

0.0653

Hom.:

2490

Bravo

AF:

0.125

Asia WGS

AF:

0.109

AC:

381

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.10

(source)

DANN

Benign

0.32

PhyloP100

-0.72

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