5-84066474-C-T

Variant names:

• chr5-84066474-C-T
• rs1271160706
• NM_005711.5:c.784G>A

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_005711.5(EDIL3):​c.784G>A​(p.Val262Met) variant causes a missense change. 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V262L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: EDIL3 NM_005711.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.79
• Publications: 0 publications found

Genes affected

EDIL3 (HGNC:3173): (EGF like repeats and discoidin domains 3) The protein encoded by this gene is an integrin ligand. It plays an important role in mediating angiogenesis and may be important in vessel wall remodeling and development. It also influences endothelial cell behavior. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.3520433).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EDIL3	NM_005711.5	c.784G>A	p.Val262Met	missense_variant	Exon 7 of 11	ENST00000296591.10	NP_005702.3
EDIL3	NM_001278642.1	c.754G>A	p.Val252Met	missense_variant	Exon 6 of 10		NP_001265571.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EDIL3	ENST00000296591.10	c.784G>A	p.Val262Met	missense_variant	Exon 7 of 11	1	NM_005711.5	ENSP00000296591.4
EDIL3	ENST00000380138.3	c.754G>A	p.Val252Met	missense_variant	Exon 6 of 10	1		ENSP00000369483.3
EDIL3	ENST00000510271.1	n.333G>A		non_coding_transcript_exon_variant	Exon 2 of 5	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Pathogenic	0.20	D
BayesDel_noAF	Uncertain	0.040
CADD	Uncertain	23
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.57	D;.
Eigen	Uncertain	0.33
Eigen_PC	Uncertain	0.48
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.87	D;D
M_CAP	Uncertain	0.11	D
MetaRNN	Benign	0.35	T;T
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Benign	2.0	M;.
PhyloP100		5.8
PrimateAI	Benign	0.41	T
PROVEAN	Benign	-0.48	N;N
REVEL	Uncertain	0.48
Sift	Benign	0.10	T;T
Sift4G	Benign	0.11	T;T
Polyphen		0.28	B;B
Vest4		0.38
MutPred		0.48		Loss of methylation at K261 (P = 0.024);.;
MVP		0.98
MPC		0.70
ClinPred		0.94	D
GERP RS		6.1
Varity_R		0.074
gMVP		0.41
Mutation Taster		=69/31	polymorphism

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: rs1271160706; hg19: chr5-83362293;