2-158826494-CATATATATATAT-CATATATATATATATATAT

Variant names:

• chr2-158826494-C-CATATAT
• rs750057852
• ENST00000343761.4:c.224+7_224+8insATATAT

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+8insATATAT 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 0.0013 (10 hom., cov: 14)
  • Exomes 𝑓: 0.00012 (2 hom.)
• Consequence: DAPL1 ENST00000343761.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 10 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+8insATATAT		splice_region intron	N/A	ENSP00000385306.2	H0Y3U5
	DAPL1	ENST00000409042.5	TSL:4	c.299+7_299+8insATATAT		splice_region intron	N/A	ENSP00000386422.1	B8ZZC6

Frequencies

GnomAD3 genomes AF: 0.00126 AC: 76 AN: 60288 Hom.: 10 Cov.: 14

Gnomad AFR AF: 0.00327

Gnomad AMI AF: 0.00709

Gnomad AMR AF: 0.00175

Gnomad ASJ AF: 0.000621

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000281

Gnomad OTH AF: 0.00139

GnomAD4 exome AF: 0.000119 AC: 24 AN: 201828 Hom.: 2 Cov.: 1 AF XY: 0.000127 AC XY: 14 AN XY: 110018

African (AFR) AF: 0.000663 AC: 4 AN: 6034

American (AMR) AF: 0.00 AC: 0 AN: 7742

Ashkenazi Jewish (ASJ) AF: 0.000796 AC: 4 AN: 5024

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

South Asian (SAS) AF: 0.000233 AC: 4 AN: 17140

European-Finnish (FIN) AF: 0.000174 AC: 3 AN: 17236

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 730

European-Non Finnish (NFE) AF: 0.0000710 AC: 9 AN: 126796

Other (OTH) AF: 0.00 AC: 0 AN: 9010

GnomAD4 genome AF: 0.00128 AC: 77 AN: 60330 Hom.: 10 Cov.: 14 AF XY: 0.00156 AC XY: 43 AN XY: 27508

African (AFR) AF: 0.00332 AC: 55 AN: 16570

American (AMR) AF: 0.00175 AC: 10 AN: 5718

Ashkenazi Jewish (ASJ) AF: 0.000621 AC: 1 AN: 1610

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

South Asian (SAS) AF: 0.00 AC: 0 AN: 1996

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

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 74

European-Non Finnish (NFE) AF: 0.000281 AC: 8 AN: 28514

Other (OTH) AF: 0.00135 AC: 1 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		-0.092

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;