Genetic Variant ENSG00000229642:n.292-8787T>A (chr3-5734877-T-A) – 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.292-8787T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,232 control chromosomes in the GnomAD database, including 1,916 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 0.13 ( 1916 hom., cov: 33)

Consequence

ENSG00000229642
ENST00000425894.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.713

Publications

1 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 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.292-8787T>A	intron_variant	Intron 2 of 8	3
ENSG00000229642	ENST00000779001.1 link	n.212+38391T>A	intron_variant	Intron 2 of 7
ENSG00000229642	ENST00000779002.1 link	n.232+38391T>A	intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19239

AN:

152114

Hom.:

1905

Cov.:

show subpopulations

Gnomad AFR

AF:

0.274

Gnomad AMI

AF:

0.0757

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.0717

Gnomad EAS

AF:

0.178

Gnomad SAS

AF:

0.0366

Gnomad FIN

AF:

0.0602

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.0574

Gnomad OTH

AF:

0.124

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

GnomAD4 genome

AF:

0.127

AC:

19292

AN:

152232

Hom.:

1916

Cov.:

AF XY:

0.124

AC XY:

9254

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.275

AC:

11399

AN:

41510

American (AMR)

AF:

0.107

AC:

1635

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0717

AC:

249

AN:

3472

East Asian (EAS)

AF:

0.178

AC:

919

AN:

5174

South Asian (SAS)

AF:

0.0362

AC:

175

AN:

4832

European-Finnish (FIN)

AF:

0.0602

AC:

639

AN:

10614

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0574

AC:

3902

AN:

68018

Other (OTH)

AF:

0.126

AC:

267

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

824

1648

2471

3295

4119

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

198

396

594

792

990

<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:

0.102

Hom.:

144

Bravo

AF:

0.141

Asia WGS

AF:

0.115

AC:

401

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.0

(source)

DANN

Benign

0.35

PhyloP100

0.71

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