2-158826494-C-CATATATATATATATAT

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The ENST00000343761.4(DAPL1):c.225+8_225+23dup variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0021 (16 hom., cov: 14)
  • Exomes 𝑓: 0.0023 (92 hom.)
  • Failed GnomAD Quality Control
• Consequence: DAPL1 ENST00000343761.4 splice_region, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• 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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 2-158826494-C-CATATATATATATATAT is Benign according to our data. Variant chr2-158826494-C-CATATATATATATATAT is described in ClinVar as [Likely_benign]. Clinvar id is 2651449.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd at 16 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAPL1	ENST00000343761.4	c.225+8_225+23dup		splice_region_variant, intron_variant		3
DAPL1	ENST00000409042.5	c.299+8_299+23dup		splice_region_variant, intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.00212 AC: 128 AN: 60264 Hom.: 16 Cov.: 14

Gnomad AFR AF: 0.00218

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000351

Gnomad ASJ AF: 0.00559

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000996

Gnomad FIN AF: 0.000954

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00263

Gnomad OTH AF: 0.00418

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00226 AC: 456 AN: 201674 Hom.: 92 Cov.: 1 AF XY: 0.00230 AC XY: 253 AN XY: 109946

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000517

Gnomad4 ASJ exome AF: 0.00159

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000583

Gnomad4 FIN exome AF: 0.0160

Gnomad4 NFE exome AF: 0.00123

Gnomad4 OTH exome AF: 0.000555

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00212 AC: 128 AN: 60304 Hom.: 16 Cov.: 14 AF XY: 0.00200 AC XY: 55 AN XY: 27500

Gnomad4 AFR AF: 0.00217

Gnomad4 AMR AF: 0.000350

Gnomad4 ASJ AF: 0.00559

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00100

Gnomad4 FIN AF: 0.000954

Gnomad4 NFE AF: 0.00263

Gnomad4 OTH AF: 0.00408

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

DAPL1: BS2 -

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;