Genetic Variant ENSG00000286856:n.139-26089A>G (chr3-170968784-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000655926.1(ENSG00000286856):n.139-26089A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 151,904 control chromosomes in the GnomAD database, including 1,686 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 0.14 ( 1686 hom., cov: 31)

Consequence

ENSG00000286856
ENST00000655926.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.186

Publications

6 publications found

Variant links:

Genes affected

ENSG00000286856 (HGNC:):

ENSG00000286856 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286856	ENST00000655926.1 link	n.139-26089A>G	intron_variant	Intron 1 of 2
ENSG00000286856	ENST00000834079.1 link	n.157-26089A>G	intron_variant	Intron 1 of 3
ENSG00000286856	ENST00000834080.1 link	n.324-26089A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.144

AC:

21820

AN:

151786

Hom.:

1688

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.168

Gnomad AMR

AF:

0.158

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.197

Gnomad SAS

AF:

0.0970

Gnomad FIN

AF:

0.115

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.155

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

GnomAD4 genome

AF:

0.144

AC:

21807

AN:

151904

Hom.:

1686

Cov.:

AF XY:

0.141

AC XY:

10449

AN XY:

74212

show subpopulations

African (AFR)

AF:

0.115

AC:

4772

AN:

41422

American (AMR)

AF:

0.158

AC:

2404

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.181

AC:

628

AN:

3466

East Asian (EAS)

AF:

0.196

AC:

1012

AN:

5152

South Asian (SAS)

AF:

0.0970

AC:

465

AN:

4792

European-Finnish (FIN)

AF:

0.115

AC:

1216

AN:

10560

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.159

AC:

10791

AN:

67966

Other (OTH)

AF:

0.152

AC:

318

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

908

1816

2725

3633

4541

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

240

480

720

960

1200

<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:

0.155

Hom.:

997

Bravo

AF:

0.148

Asia WGS

AF:

0.150

AC:

518

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.9

(source)

DANN

Benign

0.32

PhyloP100

-0.19

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