Genetic Variant ENSG00000286670:n.113+35659A>G (chr9-2710639-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000768783.1(ENSG00000286670):n.113+35659A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,052 control chromosomes in the GnomAD database, including 6,759 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 0.29 ( 6759 hom., cov: 31)

Consequence

ENSG00000286670
ENST00000768783.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.38

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286670 (HGNC:):

ENSG00000286670 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=-0.68).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286670	ENST00000768783.1 link	n.113+35659A>G	intron_variant	Intron 1 of 3
ENSG00000286670	ENST00000768784.1 link	n.156+21306A>G	intron_variant	Intron 1 of 3
ENSG00000286670	ENST00000768785.1 link	n.156+21306A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.292

AC:

44407

AN:

151934

Hom.:

6756

Cov.:

show subpopulations

Gnomad AFR

AF:

0.256

Gnomad AMI

AF:

0.263

Gnomad AMR

AF:

0.249

Gnomad ASJ

AF:

0.399

Gnomad EAS

AF:

0.131

Gnomad SAS

AF:

0.368

Gnomad FIN

AF:

0.331

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.319

Gnomad OTH

AF:

0.315

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

GnomAD4 genome

AF:

0.292

AC:

44431

AN:

152052

Hom.:

6759

Cov.:

AF XY:

0.291

AC XY:

21637

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.256

AC:

10633

AN:

41470

American (AMR)

AF:

0.248

AC:

3794

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.399

AC:

1382

AN:

3466

East Asian (EAS)

AF:

0.132

AC:

680

AN:

5160

South Asian (SAS)

AF:

0.368

AC:

1775

AN:

4820

European-Finnish (FIN)

AF:

0.331

AC:

3507

AN:

10582

Middle Eastern (MID)

AF:

0.371

AC:

109

AN:

294

European-Non Finnish (NFE)

AF:

0.319

AC:

21651

AN:

67968

Other (OTH)

AF:

0.313

AC:

660

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1597

3195

4792

6390

7987

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

466

932

1398

1864

2330

<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:

0.270

Hom.:

2048

Bravo

AF:

0.283

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

(source)

DANN

Benign

0.74

PhyloP100

1.4

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