Genetic Variant ENSG00000286791:n.391-14077C>T (chr12-127239387-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 ENST00000755538.1(ENSG00000286791):n.391-14077C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0269 in 152,282 control chromosomes in the GnomAD database, including 70 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 0.027 ( 70 hom., cov: 33)

Consequence

ENSG00000286791
ENST00000755538.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.149

Publications

1 publications found

Variant links:

COSMIC-nc: COSV107991108

Genes affected

ENSG00000286791 (HGNC:):

ENSG00000286791 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 (SAS) allele frequency at 95% confidence interval = 0.0584 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
ENSG00000286791	ENST00000755538.1 link	n.391-14077C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0270

AC:

4105

AN:

152164

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00664

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0171

Gnomad ASJ

AF:

0.0490

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0642

Gnomad FIN

AF:

0.0281

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0398

Gnomad OTH

AF:

0.0301

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

GnomAD4 genome

AF:

0.0269

AC:

4103

AN:

152282

Hom.:

Cov.:

AF XY:

0.0267

AC XY:

1986

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.00662

AC:

275

AN:

41558

American (AMR)

AF:

0.0171

AC:

261

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0490

AC:

170

AN:

3470

East Asian (EAS)

AF:

0.000386

AC:

AN:

5180

South Asian (SAS)

AF:

0.0642

AC:

310

AN:

4826

European-Finnish (FIN)

AF:

0.0281

AC:

298

AN:

10610

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0398

AC:

2710

AN:

68024

Other (OTH)

AF:

0.0298

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

208

415

623

830

1038

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0290

Hom.:

Bravo

AF:

0.0236

Asia WGS

AF:

0.0230

AC:

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

4.1

(source)

DANN

Benign

0.39

PhyloP100

-0.15

Splicing

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

Publications

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12-127239387-C-T

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