5-84064838-G-C

Variant names:

• chr5-84064838-G-C
• rs752603385
• NM_005711.5:c.814C>G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_005711.5(EDIL3):​c.814C>G​(p.Arg272Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000000687 in 1,455,932 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R272C) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: EDIL3 NM_005711.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.95
• 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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005711.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EDIL3	NM_005711.5	MANE Select	c.814C>G	p.Arg272Gly	missense	Exon 8 of 11	NP_005702.3
	EDIL3	NM_001278642.1		c.784C>G	p.Arg262Gly	missense	Exon 7 of 10	NP_001265571.1	O43854-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EDIL3	ENST00000296591.10	TSL:1 MANE Select	c.814C>G	p.Arg272Gly	missense	Exon 8 of 11	ENSP00000296591.4	O43854-1
	EDIL3	ENST00000380138.3	TSL:1	c.784C>G	p.Arg262Gly	missense	Exon 7 of 10	ENSP00000369483.3	O43854-2
	EDIL3	ENST00000866584.1		c.808C>G	p.Arg270Gly	missense	Exon 8 of 11	ENSP00000536643.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.87e-7 AC: 1 AN: 1455932 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 723908

African (AFR) AF: 0.00 AC: 0 AN: 33248

American (AMR) AF: 0.00 AC: 0 AN: 43648

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25864

East Asian (EAS) AF: 0.00 AC: 0 AN: 39598

South Asian (SAS) AF: 0.00 AC: 0 AN: 84782

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53338

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5732

European-Non Finnish (NFE) AF: 9.01e-7 AC: 1 AN: 1109588

Other (OTH) AF: 0.00 AC: 0 AN: 60134

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.080
CADD	Benign	22
DANN	Benign	0.87
DEOGEN2	Uncertain	0.54	D
Eigen	Benign	-0.085
Eigen_PC	Benign	0.069
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.88	D
M_CAP	Uncertain	0.24	D
MetaRNN	Uncertain	0.72	D
MetaSVM	Uncertain	0.66	D
MutationAssessor	Benign	1.5	L
PhyloP100		5.9
PrimateAI	Benign	0.24	T
PROVEAN	Benign	-0.94	N
REVEL	Uncertain	0.55
Sift	Benign	0.40	T
Sift4G	Benign	0.42	T
Polyphen		0.012	B
Vest4		0.69
MutPred		0.43		Loss of catalytic residue at R272 (P = 0.012)
MVP		0.97
MPC		0.46
ClinPred		0.85	D
GERP RS		5.5
Varity_R		0.19
gMVP		0.52
Mutation Taster		=62/38	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: rs752603385; hg19: chr5-83360657;