chr2-158826494-C-CATATATATATATATATATATATAT

Variant names:

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

Variant summary

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

The ENST00000343761.4(DAPL1):​c.224+7_224+8insATATATATATATATATATATATAT 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 0.0040 (26 hom., cov: 14)
  • Exomes 𝑓: 0.0012 (70 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 70 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+8insATATATATATATATATATATATAT		splice_region_variant, intron_variant	Intron 3 of 3	3		ENSP00000385306.2
DAPL1	ENST00000409042.5	c.299+7_299+8insATATATATATATATATATATATAT		splice_region_variant, intron_variant	Intron 4 of 4	4		ENSP00000386422.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 238 AN: 60182 Hom.: 26 Cov.: 14 FAILED QC

Gnomad AFR AF: 0.00388

Gnomad AMI AF: 0.00709

Gnomad AMR AF: 0.00298

Gnomad ASJ AF: 0.00436

Gnomad EAS AF: 0.00132

Gnomad SAS AF: 0.00349

Gnomad FIN AF: 0.000956

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00467

Gnomad OTH AF: 0.00278

GnomAD4 exome AF: 0.00124 AC: 250 AN: 201766 Hom.: 70 Cov.: 1 AF XY: 0.00108 AC XY: 119 AN XY: 109988

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.000398

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0107

Gnomad4 NFE exome AF: 0.000513

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00395 AC: 238 AN: 60224 Hom.: 26 Cov.: 14 AF XY: 0.00408 AC XY: 112 AN XY: 27470

Gnomad4 AFR AF: 0.00387

Gnomad4 AMR AF: 0.00298

Gnomad4 ASJ AF: 0.00436

Gnomad4 EAS AF: 0.00132

Gnomad4 SAS AF: 0.00352

Gnomad4 FIN AF: 0.000956

Gnomad4 NFE AF: 0.00467

Gnomad4 OTH AF: 0.00270

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;