2-158826494-CATATATATATAT-CATATATAT

Variant names:

• chr2-158826494-CATAT-C
• rs750057852
• ENST00000343761.4:c.224+8_224+11delATAT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000343761.4(DAPL1):​c.224+8_224+11delATAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000423 in 262,132 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00035 (0 hom., cov: 14)
  • Exomes 𝑓: 0.00045 (1 hom.)
• Consequence: DAPL1 ENST00000343761.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.730
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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+8_224+11delATAT		splice_region intron	N/A	ENSP00000385306.2	H0Y3U5
	DAPL1	ENST00000409042.5	TSL:4	c.299+8_299+11delATAT		splice_region intron	N/A	ENSP00000386422.1	B8ZZC6

Frequencies

GnomAD3 genomes AF: 0.000348 AC: 21 AN: 60296 Hom.: 0 Cov.: 14

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000351

Gnomad ASJ AF: 0.00248

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000498

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0128

Gnomad NFE AF: 0.000456

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000446 AC: 90 AN: 201794 Hom.: 1 AF XY: 0.000500 AC XY: 55 AN XY: 110006

African (AFR) AF: 0.00 AC: 0 AN: 6034

American (AMR) AF: 0.000129 AC: 1 AN: 7736

Ashkenazi Jewish (ASJ) AF: 0.00498 AC: 25 AN: 5024

East Asian (EAS) AF: 0.00 AC: 0 AN: 12116

South Asian (SAS) AF: 0.000700 AC: 12 AN: 17140

European-Finnish (FIN) AF: 0.000290 AC: 5 AN: 17232

Middle Eastern (MID) AF: 0.00137 AC: 1 AN: 730

European-Non Finnish (NFE) AF: 0.000355 AC: 45 AN: 126776

Other (OTH) AF: 0.000111 AC: 1 AN: 9006

GnomAD4 genome AF: 0.000348 AC: 21 AN: 60338 Hom.: 0 Cov.: 14 AF XY: 0.000327 AC XY: 9 AN XY: 27516

African (AFR) AF: 0.00 AC: 0 AN: 16572

American (AMR) AF: 0.000350 AC: 2 AN: 5720

Ashkenazi Jewish (ASJ) AF: 0.00248 AC: 4 AN: 1610

East Asian (EAS) AF: 0.00 AC: 0 AN: 3778

South Asian (SAS) AF: 0.000501 AC: 1 AN: 1996

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1048

Middle Eastern (MID) AF: 0.0135 AC: 1 AN: 74

European-Non Finnish (NFE) AF: 0.000456 AC: 13 AN: 28518

Other (OTH) AF: 0.00 AC: 0 AN: 740

Alfa AF: 0.00 Hom.: 71

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.73
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs750057852; hg19: chr2-159683006;