Genetic Variant ENSG00000286147:n.486-4214T>C (chr4-106906844-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000650850.1(ENSG00000286147):n.486-4214T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,982 control chromosomes in the GnomAD database, including 7,948 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 0.32 ( 7948 hom., cov: 31)

Consequence

ENSG00000286147
ENST00000650850.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.869

Publications

4 publications found

Variant links:

Genes affected

ENSG00000286147 (HGNC:):

ENSG00000286147 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=-0.6).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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
ENSG00000286147	ENST00000650850.1 link	n.486-4214T>C		intron_variant	Intron 6 of 10

Frequencies

GnomAD3 genomes

AF:

0.318

AC:

48251

AN:

151864

Hom.:

7938

Cov.:

show subpopulations

Gnomad AFR

AF:

0.393

Gnomad AMI

AF:

0.320

Gnomad AMR

AF:

0.241

Gnomad ASJ

AF:

0.309

Gnomad EAS

AF:

0.255

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.282

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.317

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

GnomAD4 genome

AF:

0.318

AC:

48303

AN:

151982

Hom.:

7948

Cov.:

AF XY:

0.312

AC XY:

23187

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.393

AC:

16265

AN:

41436

American (AMR)

AF:

0.240

AC:

3666

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.309

AC:

1073

AN:

3468

East Asian (EAS)

AF:

0.255

AC:

1313

AN:

5150

South Asian (SAS)

AF:

0.217

AC:

1046

AN:

4816

European-Finnish (FIN)

AF:

0.282

AC:

2987

AN:

10576

Middle Eastern (MID)

AF:

0.272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.307

AC:

20901

AN:

67980

Other (OTH)

AF:

0.323

AC:

681

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1648

3295

4943

6590

8238

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

486

972

1458

1944

2430

<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:

0.285

Hom.:

4388

Bravo

AF:

0.317

Asia WGS

AF:

0.232

AC:

806

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

(source)

DANN

Benign

0.65

PhyloP100

0.87

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