chr2-158826494-C-CATATATATATAT

Variant names:

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

Variant summary

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

The ENST00000343761.4(DAPL1):​c.224+7_224+8insATATATATATAT 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 0.00038 (1 hom., cov: 14)
  • Exomes 𝑓: 0.00038 (18 hom.)
• 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 18 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+8insATATATATATAT		splice_region_variant, intron_variant	Intron 3 of 3	3		ENSP00000385306.2
DAPL1	ENST00000409042.5	c.299+7_299+8insATATATATATAT		splice_region_variant, intron_variant	Intron 4 of 4	4		ENSP00000386422.1

Frequencies

GnomAD3 genomes AF: 0.000382 AC: 23 AN: 60284 Hom.: 1 Cov.: 14

Gnomad AFR AF: 0.000424

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000351

Gnomad ASJ AF: 0.000621

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000498

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000421

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000377 AC: 76 AN: 201828 Hom.: 18 Cov.: 1 AF XY: 0.000373 AC XY: 41 AN XY: 110020

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000904

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000350

Gnomad4 FIN exome AF: 0.00168

Gnomad4 NFE exome AF: 0.000252

Gnomad4 OTH exome AF: 0.000222

GnomAD4 genome AF: 0.000381 AC: 23 AN: 60326 Hom.: 1 Cov.: 14 AF XY: 0.000291 AC XY: 8 AN XY: 27516

Gnomad4 AFR AF: 0.000423

Gnomad4 AMR AF: 0.000350

Gnomad4 ASJ AF: 0.000621

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000501

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000421

Gnomad4 OTH AF: 0.00

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;