2-158826494-CATATATATATAT-CATATATATATATATATATATATATATATATATATATAT

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The ENST00000343761.4(DAPL1):​c.224+7_224+8insATATATATATATATATATATATATAT 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 0.0039 (27 hom., cov: 14)
  • Exomes 𝑓: 0.00076 (42 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAdExome4 at 42 AR gene

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+8insATATATATATATATATATATATATAT		splice_region_variant, intron_variant	Intron 3 of 3	3		ENSP00000385306.2
DAPL1	ENST00000409042.5	c.299+7_299+8insATATATATATATATATATATATATAT		splice_region_variant, intron_variant	Intron 4 of 4	4		ENSP00000386422.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 235 AN: 60188 Hom.: 27 Cov.: 14 FAILED QC

Gnomad AFR AF: 0.00539

Gnomad AMI AF: 0.00709

Gnomad AMR AF: 0.00123

Gnomad ASJ AF: 0.00436

Gnomad EAS AF: 0.000264

Gnomad SAS AF: 0.00498

Gnomad FIN AF: 0.00191

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00408

Gnomad OTH AF: 0.00139

GnomAD4 exome AF: 0.000758 AC: 153 AN: 201796 Hom.: 42 Cov.: 1 AF XY: 0.000764 AC XY: 84 AN XY: 110008

Gnomad4 AFR exome AF: 0.000166

Gnomad4 AMR exome AF: 0.000258

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00662

Gnomad4 NFE exome AF: 0.000284

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00390 AC: 235 AN: 60230 Hom.: 27 Cov.: 14 AF XY: 0.00339 AC XY: 93 AN XY: 27466

Gnomad4 AFR AF: 0.00538

Gnomad4 AMR AF: 0.00123

Gnomad4 ASJ AF: 0.00436

Gnomad4 EAS AF: 0.000265

Gnomad4 SAS AF: 0.00501

Gnomad4 FIN AF: 0.00191

Gnomad4 NFE AF: 0.00408

Gnomad4 OTH AF: 0.00135

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;