Genetic Variant DAPL1:c.224+7_224+8insAT (chr2-158826494-C-CAT) – 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+8insAT 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 0.0024 ( 8 hom., cov: 14)

Exomes 𝑓: 0.0043 ( 27 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:

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ACMG classification

Classification was made for transcript

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

BS2

High Homozygotes in GnomAd4 at 8 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+8insAT		splice_region intron	N/A	ENSP00000385306.2	H0Y3U5
	DAPL1	ENST00000409042.5	TSL:4	c.299+7_299+8insAT		splice_region intron	N/A	ENSP00000386422.1	B8ZZC6

Frequencies

GnomAD3 genomes

AF:

0.00239

AC:

144

AN:

60284

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00175

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00105

Gnomad ASJ

AF:

0.000621

Gnomad EAS

AF:

0.0127

Gnomad SAS

AF:

0.00697

Gnomad FIN

AF:

0.00191

Gnomad MID

AF:

0.0128

Gnomad NFE

AF:

0.00140

Gnomad OTH

AF:

0.00417

GnomAD4 exome

AF:

0.00432

AC:

872

AN:

201624

Hom.:

Cov.:

AF XY:

0.00439

AC XY:

483

AN XY:

109934

show subpopulations

African (AFR)

AF:

0.00116

AC:

AN:

6034

American (AMR)

AF:

0.00233

AC:

AN:

7736

Ashkenazi Jewish (ASJ)

AF:

0.00319

AC:

AN:

5020

East Asian (EAS)

AF:

0.00471

AC:

AN:

12096

South Asian (SAS)

AF:

0.00806

AC:

138

AN:

17130

European-Finnish (FIN)

AF:

0.0217

AC:

372

AN:

17120

Middle Eastern (MID)

AF:

0.00137

AC:

AN:

730

European-Non Finnish (NFE)

AF:

0.00181

AC:

230

AN:

126752

Other (OTH)

AF:

0.00366

AC:

AN:

9006

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

110

137

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.00237

AC:

143

AN:

60326

Hom.:

Cov.:

AF XY:

0.00262

AC XY:

AN XY:

27512

show subpopulations

African (AFR)

AF:

0.00175

AC:

AN:

16566

American (AMR)

AF:

0.00105

AC:

AN:

5720

Ashkenazi Jewish (ASJ)

AF:

0.000621

AC:

AN:

1610

East Asian (EAS)

AF:

0.0124

AC:

AN:

3776

South Asian (SAS)

AF:

0.00701

AC:

AN:

1996

European-Finnish (FIN)

AF:

0.00191

AC:

AN:

1048

Middle Eastern (MID)

AF:

0.0135

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00140

AC:

AN:

28514

Other (OTH)

AF:

0.00405

AC:

AN:

740

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

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:

0.00375

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.092

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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2-158826494-CATATATATATAT-CATATATATATATAT

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