Genetic Variant ENSG00000293096:n.132+26234T>G (chr12-87757000-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000841431.1(ENSG00000293096):n.132+26234T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,232 control chromosomes in the GnomAD database, including 1,026 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 0.11 ( 1026 hom., cov: 32)

Consequence

ENSG00000293096
ENST00000841431.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0200

Publications

1 publications found

Variant links:

Genes affected

ENSG00000293096 (HGNC:):

ENSG00000293096 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=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293096	ENST00000841431.1 link	n.132+26234T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.111

AC:

16925

AN:

152114

Hom.:

1020

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0751

Gnomad AMI

AF:

0.0461

Gnomad AMR

AF:

0.155

Gnomad ASJ

AF:

0.116

Gnomad EAS

AF:

0.0417

Gnomad SAS

AF:

0.109

Gnomad FIN

AF:

0.139

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.126

Gnomad OTH

AF:

0.103

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

GnomAD4 genome

AF:

0.111

AC:

16951

AN:

152232

Hom.:

1026

Cov.:

AF XY:

0.114

AC XY:

8490

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.0752

AC:

3126

AN:

41560

American (AMR)

AF:

0.155

AC:

2366

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.116

AC:

402

AN:

3468

East Asian (EAS)

AF:

0.0415

AC:

214

AN:

5162

South Asian (SAS)

AF:

0.108

AC:

523

AN:

4828

European-Finnish (FIN)

AF:

0.139

AC:

1467

AN:

10592

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.126

AC:

8563

AN:

68008

Other (OTH)

AF:

0.108

AC:

228

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

761

1521

2282

3042

3803

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

392

588

784

980

<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:

0.0815

Hom.:

144

Bravo

AF:

0.109

Asia WGS

AF:

0.153

AC:

529

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.6

(source)

DANN

Benign

0.41

PhyloP100

-0.020

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