Genetic Variant ENSG00000289559:n.857-35C>T (chr6-32891971-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 ENST00000753352.1(ENSG00000289559):n.857-35C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,150 control chromosomes in the GnomAD database, including 1,453 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 ( 1453 hom., cov: 32)

Consequence

ENSG00000289559
ENST00000753352.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.395

Publications

9 publications found

Variant links:

Genes affected

ENSG00000289559 (HGNC:):

ENSG00000289559 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000289559	ENST00000753352.1 link	n.857-35C>T	intron_variant	Intron 2 of 2
ENSG00000289559	ENST00000753353.1 link	n.508-35C>T	intron_variant	Intron 2 of 2
ENSG00000289559	ENST00000753354.1 link	n.416-35C>T	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.129

AC:

19603

AN:

152032

Hom.:

1447

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.0746

Gnomad AMR

AF:

0.0952

Gnomad ASJ

AF:

0.184

Gnomad EAS

AF:

0.0867

Gnomad SAS

AF:

0.142

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.119

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

GnomAD4 genome

AF:

0.129

AC:

19647

AN:

152150

Hom.:

1453

Cov.:

AF XY:

0.130

AC XY:

9642

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.193

AC:

8023

AN:

41494

American (AMR)

AF:

0.0952

AC:

1455

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.184

AC:

639

AN:

3468

East Asian (EAS)

AF:

0.0867

AC:

450

AN:

5188

South Asian (SAS)

AF:

0.142

AC:

684

AN:

4822

European-Finnish (FIN)

AF:

0.114

AC:

1203

AN:

10580

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.101

AC:

6835

AN:

67994

Other (OTH)

AF:

0.121

AC:

255

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

854

1708

2563

3417

4271

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

208

416

624

832

1040

<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:

0.109

Hom.:

525

Bravo

AF:

0.128

Asia WGS

AF:

0.141

AC:

490

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.6

(source)

DANN

Benign

0.68

PhyloP100

-0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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