rs748615283

Variant names:

• chr2-158807734-A-C
• rs748615283
• ENST00000621326.4:c.270A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-158807734-A-C
• chr2-158807734-A-G

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The ENST00000621326.4(DAPL1):​c.270A>C​(p.Pro90Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P90P) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DAPL1 ENST00000621326.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

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 -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP7: Synonymous conserved (PhyloP=0.347 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAPL1	NM_001017920.3	c.207+619A>C		intron_variant	Intron 3 of 3	ENST00000309950.8	NP_001017920.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAPL1	ENST00000621326.4	c.270A>C	p.Pro90Pro	synonymous_variant	Exon 4 of 5	1		ENSP00000479872.1
DAPL1	ENST00000309950.8	c.207+619A>C		intron_variant	Intron 3 of 3	1	NM_001017920.3	ENSP00000309538.4
DAPL1	ENST00000343761.4	c.132+619A>C		intron_variant	Intron 2 of 3	3		ENSP00000385306.2
DAPL1	ENST00000409042.5	c.207+619A>C		intron_variant	Intron 3 of 4	4		ENSP00000386422.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.77

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: rs748615283; hg19: chr2-159664246;