Genetic Variant ENST00000653528.1:n.203-14292T>G (chr6-67981742-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000653528.1(ENSG00000286680):n.203-14292T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,004 control chromosomes in the GnomAD database, including 1,795 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 0.15 ( 1795 hom., cov: 32)

Consequence

ENSG00000286680
ENST00000653528.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.767

Publications

4 publications found

Variant links:

Genes affected

ENSG00000286680 (HGNC:):

ENSG00000286680 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=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286680	ENST00000653528.1 link	n.203-14292T>G	intron_variant	Intron 2 of 3
ENSG00000286680	ENST00000661401.1 link	n.317-4508T>G	intron_variant	Intron 3 of 3
ENSG00000286680	ENST00000718119.1 link	n.254-4508T>G	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22792

AN:

151886

Hom.:

1796

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.122

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.166

Gnomad EAS

AF:

0.0471

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.138

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.191

Gnomad OTH

AF:

0.148

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

GnomAD4 genome

AF:

0.150

AC:

22796

AN:

152004

Hom.:

1795

Cov.:

AF XY:

0.146

AC XY:

10866

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.111

AC:

4623

AN:

41484

American (AMR)

AF:

0.127

AC:

1932

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.166

AC:

575

AN:

3466

East Asian (EAS)

AF:

0.0474

AC:

244

AN:

5152

South Asian (SAS)

AF:

0.113

AC:

546

AN:

4826

European-Finnish (FIN)

AF:

0.138

AC:

1463

AN:

10602

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.191

AC:

12952

AN:

67922

Other (OTH)

AF:

0.146

AC:

307

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

992

1984

2977

3969

4961

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.175

Hom.:

6371

Bravo

AF:

0.148

Asia WGS

AF:

0.0850

AC:

296

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.85

(source)

DANN

Benign

0.79

PhyloP100

-0.77

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