Genetic Variant ENST00000650201.1:n.113+39925G>A (chr18-60369270-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000650201.1(ENSG00000285681):n.113+39925G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,012 control chromosomes in the GnomAD database, including 8,780 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 0.33 ( 8780 hom., cov: 32)

Consequence

ENSG00000285681
ENST00000650201.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.84

Publications

12 publications found

Variant links:

Genes affected

ENSG00000285681 (HGNC:):

ENSG00000285681 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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 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
ENSG00000285681	ENST00000650201.1 link	n.113+39925G>A		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1 link	n.156+39925G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.327

AC:

49673

AN:

151894

Hom.:

8754

Cov.:

show subpopulations

Gnomad AFR

AF:

0.450

Gnomad AMI

AF:

0.373

Gnomad AMR

AF:

0.287

Gnomad ASJ

AF:

0.229

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.279

Gnomad FIN

AF:

0.216

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.302

Gnomad OTH

AF:

0.317

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

GnomAD4 genome

AF:

0.327

AC:

49734

AN:

152012

Hom.:

8780

Cov.:

AF XY:

0.319

AC XY:

23705

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.451

AC:

18672

AN:

41432

American (AMR)

AF:

0.286

AC:

4369

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.229

AC:

794

AN:

3470

East Asian (EAS)

AF:

0.127

AC:

655

AN:

5170

South Asian (SAS)

AF:

0.277

AC:

1336

AN:

4820

European-Finnish (FIN)

AF:

0.216

AC:

2285

AN:

10566

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.302

AC:

20543

AN:

67972

Other (OTH)

AF:

0.315

AC:

665

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1648

3297

4945

6594

8242

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

494

988

1482

1976

2470

<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:

0.315

Hom.:

19531

Bravo

AF:

0.344

Asia WGS

AF:

0.209

AC:

728

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.023

(source)

DANN

Benign

0.23

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