Genetic Variant DAPL1:c.224+7_224+8insATATATAT (chr2-158826494-C-CATATATAT) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The ENST00000343761.4(DAPL1):c.224+7_224+8insATATATAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000083 ( 0 hom., cov: 14)

Exomes 𝑓: 0.00024 ( 6 hom. )

Consequence

DAPL1
ENST00000343761.4 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0920

Publications

0 publications found

Variant links:

Genes affected

DAPL1 (HGNC:21490): (death associated protein like 1) Predicted to enable death domain binding activity. Predicted to be involved in apoptotic signaling pathway; cellular response to amino acid starvation; and negative regulation of autophagy. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

DAPL1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 6 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000343761.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAPL1	ENST00000343761.4	TSL:3	c.224+7_224+8insATATATAT		splice_region intron	N/A	ENSP00000385306.2	H0Y3U5
	DAPL1	ENST00000409042.5	TSL:4	c.299+7_299+8insATATATAT		splice_region intron	N/A	ENSP00000386422.1	B8ZZC6

Frequencies

GnomAD3 genomes

AF:

0.0000663

AC:

AN:

60292

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000605

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000498

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000701

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000238

AC:

AN:

201820

Hom.:

Cov.:

AF XY:

0.000273

AC XY:

AN XY:

110018

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

6034

American (AMR)

AF:

0.000387

AC:

AN:

7742

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

5024

East Asian (EAS)

AF:

0.00

AC:

AN:

12116

South Asian (SAS)

AF:

0.000525

AC:

AN:

17138

European-Finnish (FIN)

AF:

0.000464

AC:

AN:

17234

Middle Eastern (MID)

AF:

0.00137

AC:

AN:

730

European-Non Finnish (NFE)

AF:

0.000213

AC:

AN:

126792

Other (OTH)

AF:

0.00

AC:

AN:

9010

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.437

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000829

AC:

AN:

60334

Hom.:

Cov.:

AF XY:

0.0000727

AC XY:

AN XY:

27516

show subpopulations

African (AFR)

AF:

0.0000603

AC:

AN:

16572

American (AMR)

AF:

0.00

AC:

AN:

5720

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1610

East Asian (EAS)

AF:

0.00

AC:

AN:

3778

South Asian (SAS)

AF:

0.000501

AC:

AN:

1996

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1048

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0000701

AC:

AN:

28514

Other (OTH)

AF:

0.00135

AC:

AN:

740

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.092

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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2-158826494-CATATATATATAT-CATATATATATATATATATAT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over