Genetic Variant ENSG00000286840:n.269+4297C>T (chr9-73543766-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 ENST00000667966.1(ENSG00000286840):n.269+4297C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,028 control chromosomes in the GnomAD database, including 1,482 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 0.12 ( 1482 hom., cov: 33)

Consequence

ENSG00000286840
ENST00000667966.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.154

Publications

10 publications found

Variant links:

Genes affected

ENSG00000286840 (HGNC:):

ENSG00000286840 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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286840	ENST00000667966.1 link	n.269+4297C>T	intron_variant	Intron 1 of 3
ENSG00000232590	ENST00000715871.1 link	n.182-34103G>A	intron_variant	Intron 2 of 2
ENSG00000232590	ENST00000715872.1 link	n.196-59598G>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18906

AN:

151910

Hom.:

1477

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0311

Gnomad AMI

AF:

0.141

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.151

Gnomad EAS

AF:

0.0975

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.153

Gnomad MID

AF:

0.204

Gnomad NFE

AF:

0.170

Gnomad OTH

AF:

0.159

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

GnomAD4 genome

AF:

0.124

AC:

18916

AN:

152028

Hom.:

1482

Cov.:

AF XY:

0.125

AC XY:

9296

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.0310

AC:

1288

AN:

41536

American (AMR)

AF:

0.139

AC:

2116

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.151

AC:

522

AN:

3464

East Asian (EAS)

AF:

0.0970

AC:

502

AN:

5176

South Asian (SAS)

AF:

0.161

AC:

779

AN:

4828

European-Finnish (FIN)

AF:

0.153

AC:

1609

AN:

10536

Middle Eastern (MID)

AF:

0.216

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.170

AC:

11577

AN:

67912

Other (OTH)

AF:

0.157

AC:

331

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

818

1635

2453

3270

4088

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<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:

0.156

Hom.:

2783

Bravo

AF:

0.118

Asia WGS

AF:

0.104

AC:

358

AN:

3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.9

(source)

DANN

Benign

0.51

PhyloP100

-0.15

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