chr2-158826494-C-CATATATATATATATATATATAT

Variant names:

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

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000343761.4(DAPL1):​c.224+7_224+8insATATATATATATATATATATAT 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 0.0054 (50 hom., cov: 14)
  • Exomes 𝑓: 0.0033 (147 hom.)
  • Failed GnomAD Quality Control
• Consequence: DAPL1 ENST00000343761.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAPL1	ENST00000343761.4	c.224+7_224+8insATATATATATATATATATATAT		splice_region_variant, intron_variant	Intron 3 of 3	3		ENSP00000385306.2
DAPL1	ENST00000409042.5	c.299+7_299+8insATATATATATATATATATATAT		splice_region_variant, intron_variant	Intron 4 of 4	4		ENSP00000386422.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 326 AN: 60212 Hom.: 50 Cov.: 14 FAILED QC

Gnomad AFR AF: 0.00182

Gnomad AMI AF: 0.00709

Gnomad AMR AF: 0.00351

Gnomad ASJ AF: 0.00561

Gnomad EAS AF: 0.000528

Gnomad SAS AF: 0.00249

Gnomad FIN AF: 0.00382

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00875

Gnomad OTH AF: 0.00694

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00329 AC: 664 AN: 201652 Hom.: 147 Cov.: 1 AF XY: 0.00286 AC XY: 314 AN XY: 109934

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000258

Gnomad4 ASJ exome AF: 0.000796

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0347

Gnomad4 NFE exome AF: 0.000450

Gnomad4 OTH exome AF: 0.000888

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00541 AC: 326 AN: 60254 Hom.: 50 Cov.: 14 AF XY: 0.00488 AC XY: 134 AN XY: 27484

Gnomad4 AFR AF: 0.00181

Gnomad4 AMR AF: 0.00350

Gnomad4 ASJ AF: 0.00561

Gnomad4 EAS AF: 0.000529

Gnomad4 SAS AF: 0.00251

Gnomad4 FIN AF: 0.00382

Gnomad4 NFE AF: 0.00875

Gnomad4 OTH AF: 0.00676

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs750057852; hg19: chr2-159683006;