2-158803982-G-A

Position:

• chr2-158803982-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001017920.3(DAPL1):​c.59-300G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0974 in 152,186 control chromosomes in the GnomAD database, including 949 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.097 (949 hom., cov: 32)
• Consequence: DAPL1 NM_001017920.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAPL1	NM_001017920.3	c.59-300G>A		intron_variant		ENST00000309950.8	NP_001017920.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAPL1	ENST00000309950.8	c.59-300G>A		intron_variant		1	NM_001017920.3	ENSP00000309538.4
DAPL1	ENST00000621326.4	c.59-300G>A		intron_variant		1		ENSP00000479872.1
DAPL1	ENST00000409042.5	c.59-300G>A		intron_variant		4		ENSP00000386422.1

Frequencies

GnomAD3 genomes AF: 0.0975 AC: 14820 AN: 152066 Hom.: 949 Cov.: 32

Gnomad AFR AF: 0.0342

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0359

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.127

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0974 AC: 14820 AN: 152186 Hom.: 949 Cov.: 32 AF XY: 0.0974 AC XY: 7244 AN XY: 74392

Gnomad4 AFR AF: 0.0341

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0363

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.126

Alfa AF: 0.112 Hom.: 122

Bravo AF: 0.0904

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	16
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs75277023; hg19: chr2-159660494;