Genetic Variant ENST00000561596.5:n.33+37801G>C (chr11-90289118-G-C) – 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.33+37801G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0516 in 152,158 control chromosomes in the GnomAD database, including 478 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 0.052 ( 478 hom., cov: 32)

Consequence

DISC1FP1
ENST00000561596.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.868

Publications

2 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=-0.59).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DISC1FP1	NR_104190.1 link	n.86+37801G>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DISC1FP1	ENST00000561596.5 link	n.33+37801G>C	intron_variant	Intron 1 of 6	5
DISC1FP1	ENST00000562245.6 link	n.86+37801G>C	intron_variant	Intron 1 of 6	3
DISC1FP1	ENST00000649150.1 link	n.114+37801G>C	intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes

AF:

0.0516

AC:

7838

AN:

152038

Hom.:

477

Cov.:

show subpopulations

Gnomad AFR

AF:

0.147

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0226

Gnomad ASJ

AF:

0.0418

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00290

Gnomad FIN

AF:

0.00501

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0164

Gnomad OTH

AF:

0.0393

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

GnomAD4 genome

AF:

0.0516

AC:

7852

AN:

152158

Hom.:

478

Cov.:

AF XY:

0.0487

AC XY:

3624

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.147

AC:

6091

AN:

41488

American (AMR)

AF:

0.0226

AC:

345

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0418

AC:

145

AN:

3470

East Asian (EAS)

AF:

0.000386

AC:

AN:

5182

South Asian (SAS)

AF:

0.00290

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00501

AC:

AN:

10584

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0164

AC:

1112

AN:

68004

Other (OTH)

AF:

0.0389

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

347

694

1041

1388

1735

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

234

312

390

<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:

0.0394

Hom.:

Bravo

AF:

0.0579

Asia WGS

AF:

0.00982

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

(source)

DANN

Benign

0.74

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