Genetic Variant ENSG00000289621:n.423+35699A>G (chr11-58806534-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 ENST00000529451.2(ENSG00000289621):n.423+35699A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0337 in 151,974 control chromosomes in the GnomAD database, including 189 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 0.034 ( 189 hom., cov: 32)

Consequence

ENSG00000289621
ENST00000529451.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.893

Publications

2 publications found

Variant links:

Genes affected

ENSG00000289621 (HGNC:):

ENSG00000289621 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 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
ENSG00000289621	ENST00000529451.2 link	n.423+35699A>G	intron_variant	Intron 1 of 3	2
ENSG00000289621	ENST00000766632.1 link	n.421+35699A>G	intron_variant	Intron 1 of 2
ENSG00000289621	ENST00000766633.1 link	n.459+35699A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0336

AC:

5104

AN:

151856

Hom.:

187

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0267

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0442

Gnomad ASJ

AF:

0.0251

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.107

Gnomad FIN

AF:

0.0242

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0195

Gnomad OTH

AF:

0.0331

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

GnomAD4 genome

AF:

0.0337

AC:

5115

AN:

151974

Hom.:

189

Cov.:

AF XY:

0.0366

AC XY:

2720

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.0267

AC:

1109

AN:

41512

American (AMR)

AF:

0.0446

AC:

678

AN:

15206

Ashkenazi Jewish (ASJ)

AF:

0.0251

AC:

AN:

3462

East Asian (EAS)

AF:

0.208

AC:

1073

AN:

5150

South Asian (SAS)

AF:

0.106

AC:

513

AN:

4818

European-Finnish (FIN)

AF:

0.0242

AC:

257

AN:

10602

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0195

AC:

1325

AN:

67910

Other (OTH)

AF:

0.0327

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

231

462

693

924

1155

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

192

256

320

<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:

0.0103

Hom.:

Bravo

AF:

0.0360

Asia WGS

AF:

0.130

AC:

453

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

8.3

(source)

DANN

Benign

0.85

PhyloP100

0.89

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