Genetic Variant ENSG00000286147:n.485+6724C>T (chr4-106796025-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 ENST00000650850.1(ENSG00000286147):n.485+6724C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.972 in 151,658 control chromosomes in the GnomAD database, including 71,719 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 0.97 ( 71719 hom., cov: 32)

Consequence

ENSG00000286147
ENST00000650850.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.82

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286147 (HGNC:):

ENSG00000286147 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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377356	XR_939051.1 link	n.427+6724C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286147	ENST00000650850.1 link	n.485+6724C>T		intron_variant	Intron 6 of 10

Frequencies

GnomAD3 genomes

AF:

0.972

AC:

147373

AN:

151542

Hom.:

71667

Cov.:

show subpopulations

Gnomad AFR

AF:

0.978

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.976

Gnomad ASJ

AF:

0.965

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.991

Gnomad FIN

AF:

0.976

Gnomad MID

AF:

0.981

Gnomad NFE

AF:

0.964

Gnomad OTH

AF:

0.973

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

GnomAD4 genome

AF:

0.972

AC:

147482

AN:

151658

Hom.:

71719

Cov.:

AF XY:

0.974

AC XY:

72164

AN XY:

74116

show subpopulations

African (AFR)

AF:

0.978

AC:

40574

AN:

41482

American (AMR)

AF:

0.976

AC:

14797

AN:

15154

Ashkenazi Jewish (ASJ)

AF:

0.965

AC:

3335

AN:

3456

East Asian (EAS)

AF:

1.00

AC:

5133

AN:

5134

South Asian (SAS)

AF:

0.991

AC:

4774

AN:

4816

European-Finnish (FIN)

AF:

0.976

AC:

10356

AN:

10606

Middle Eastern (MID)

AF:

0.982

AC:

279

AN:

284

European-Non Finnish (NFE)

AF:

0.964

AC:

65275

AN:

67710

Other (OTH)

AF:

0.973

AC:

2047

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

208

416

623

831

1039

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

914

1828

2742

3656

4570

<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:

0.962

Hom.:

8741

Bravo

AF:

0.975

Asia WGS

AF:

0.993

AC:

3419

AN:

3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.047

(source)

DANN

Benign

0.14

PhyloP100

-1.8

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