NM_001017920.3:c.208-225A>G

Variant names:

• chr2-158815480-A-G
• rs17810816
• NM_001017920.3:c.208-225A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001017920.3(DAPL1):​c.208-225A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,220 control chromosomes in the GnomAD database, including 1,468 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency: Genomes: 𝑓 0.13 (1468 hom., cov: 33)
• Consequence: DAPL1 NM_001017920.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001017920.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAPL1	NM_001017920.3	MANE Select	c.208-225A>G		intron	N/A	NP_001017920.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAPL1	ENST00000309950.8	TSL:1 MANE Select	c.208-225A>G		intron	N/A	ENSP00000309538.4
	DAPL1	ENST00000621326.4	TSL:1	c.327-225A>G		intron	N/A	ENSP00000479872.1
	DAPL1	ENST00000343761.4	TSL:3	c.132+8365A>G		intron	N/A	ENSP00000385306.2

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19487 AN: 152102 Hom.: 1468 Cov.: 33

Gnomad AFR AF: 0.0653

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.128 AC: 19477 AN: 152220 Hom.: 1468 Cov.: 33 AF XY: 0.127 AC XY: 9464 AN XY: 74412

African (AFR) AF: 0.0651 AC: 2704 AN: 41548

American (AMR) AF: 0.126 AC: 1931 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 585 AN: 3468

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5190

South Asian (SAS) AF: 0.0670 AC: 323 AN: 4824

European-Finnish (FIN) AF: 0.197 AC: 2090 AN: 10588

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11347 AN: 67998

Other (OTH) AF: 0.168 AC: 356 AN: 2116

Alfa AF: 0.155 Hom.: 6170

Bravo AF: 0.122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.86
DANN	Benign	0.69
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17810816; hg19: chr2-159671992;