Genetic Variant ENSG00000296927:n.239-34223C>T (chr6-150458046-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000743667.1(ENSG00000296927):n.239-34223C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,032 control chromosomes in the GnomAD database, including 9,556 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 0.35 ( 9556 hom., cov: 33)

Consequence

ENSG00000296927
ENST00000743667.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0350

Publications

2 publications found

Variant links:

Genes affected

ENSG00000296927 (HGNC:):

ENSG00000296927 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000296927	ENST00000743667.1 link	n.239-34223C>T	intron_variant	Intron 1 of 2
ENSG00000296927	ENST00000743668.1 link	n.239-34223C>T	intron_variant	Intron 1 of 2
ENSG00000296927	ENST00000743669.1 link	n.203-34223C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.354

AC:

53709

AN:

151914

Hom.:

9548

Cov.:

show subpopulations

Gnomad AFR

AF:

0.353

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.349

Gnomad ASJ

AF:

0.470

Gnomad EAS

AF:

0.295

Gnomad SAS

AF:

0.353

Gnomad FIN

AF:

0.297

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.361

Gnomad OTH

AF:

0.393

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

GnomAD4 genome

AF:

0.354

AC:

53761

AN:

152032

Hom.:

9556

Cov.:

AF XY:

0.351

AC XY:

26057

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.353

AC:

14660

AN:

41474

American (AMR)

AF:

0.348

AC:

5317

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.470

AC:

1629

AN:

3464

East Asian (EAS)

AF:

0.296

AC:

1525

AN:

5156

South Asian (SAS)

AF:

0.354

AC:

1706

AN:

4818

European-Finnish (FIN)

AF:

0.297

AC:

3130

AN:

10548

Middle Eastern (MID)

AF:

0.463

AC:

136

AN:

294

European-Non Finnish (NFE)

AF:

0.361

AC:

24519

AN:

67988

Other (OTH)

AF:

0.393

AC:

830

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1823

3645

5468

7290

9113

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

532

1064

1596

2128

2660

<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:

0.363

Hom.:

4748

Bravo

AF:

0.357

Asia WGS

AF:

0.319

AC:

1107

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.6

(source)

DANN

Benign

0.50

PhyloP100

0.035

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