Genetic Variant DISC1FP1:n.279+36227G>A (chr11-90639135-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 ENST00000561596.5(DISC1FP1):n.279+36227G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,924 control chromosomes in the GnomAD database, including 18,426 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 0.48 ( 18426 hom., cov: 32)

Consequence

DISC1FP1
ENST00000561596.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.181

Publications

5 publications found

Variant links:

Genes affected

DISC1FP1 (HGNC:33625): (DISC1 fusion partner 1)

DISC1FP1 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DISC1FP1	NR_104190.1 link	n.332+36227G>A		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DISC1FP1	ENST00000561596.5 link	n.279+36227G>A	intron_variant	Intron 3 of 6	5
DISC1FP1	ENST00000562245.6 link	n.332+36227G>A	intron_variant	Intron 3 of 6	3
DISC1FP1	ENST00000562678.5 link	n.185+92240G>A	intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.481

AC:

73087

AN:

151806

Hom.:

18428

Cov.:

show subpopulations

Gnomad AFR

AF:

0.327

Gnomad AMI

AF:

0.700

Gnomad AMR

AF:

0.494

Gnomad ASJ

AF:

0.555

Gnomad EAS

AF:

0.543

Gnomad SAS

AF:

0.672

Gnomad FIN

AF:

0.449

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.552

Gnomad OTH

AF:

0.497

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

GnomAD4 genome

AF:

0.481

AC:

73105

AN:

151924

Hom.:

18426

Cov.:

AF XY:

0.481

AC XY:

35728

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.327

AC:

13528

AN:

41424

American (AMR)

AF:

0.494

AC:

7544

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.555

AC:

1922

AN:

3466

East Asian (EAS)

AF:

0.542

AC:

2794

AN:

5158

South Asian (SAS)

AF:

0.671

AC:

3231

AN:

4818

European-Finnish (FIN)

AF:

0.449

AC:

4744

AN:

10554

Middle Eastern (MID)

AF:

0.610

AC:

178

AN:

292

European-Non Finnish (NFE)

AF:

0.552

AC:

37471

AN:

67932

Other (OTH)

AF:

0.501

AC:

1055

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1876

3751

5627

7502

9378

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

680

1360

2040

2720

3400

<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:

0.531

Hom.:

16833

Bravo

AF:

0.470

Asia WGS

AF:

0.620

AC:

2154

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.95

(source)

DANN

Benign

0.16

PhyloP100

0.18

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