rs16843372

chr2-158813937-T-C

Variant summary

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

The NM_001017920.3(DAPL1):c.208-1768T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,992 control chromosomes in the GnomAD database, including 23,788 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 0.55 (23788 hom., cov: 31)
• Consequence: DAPL1 NM_001017920.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAPL1	NM_001017920.3	c.208-1768T>C		intron_variant		ENST00000309950.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAPL1	ENST00000309950.8	c.208-1768T>C		intron_variant		1	NM_001017920.3	P1
DAPL1	ENST00000621326.4	c.327-1768T>C		intron_variant		1
DAPL1	ENST00000343761.4	c.133+6822T>C		intron_variant		3
DAPL1	ENST00000409042.5	c.207+6822T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83367 AN: 151874 Hom.: 23760 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.0996

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.549 AC: 83433 AN: 151992 Hom.: 23788 Cov.: 31 AF XY: 0.544 AC XY: 40413 AN XY: 74284

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.0994

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.576

Alfa AF: 0.566 Hom.: 30227

Bravo AF: 0.535

Asia WGS AF: 0.266 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	3.2
Dann	Benign	0.80

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: rs16843372; hg19: chr2-159670449;