rs201386908

Variant names:

• chr5-84064796-T-C
• rs201386908
• NM_005711.5:c.856A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-84064796-T-C
• chr5-84064796-T-G

Variant summary

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

The NM_005711.5(EDIL3):​c.856A>G​(p.Thr286Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,582 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. T286P) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: EDIL3 NM_005711.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.61
• 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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EDIL3	NM_005711.5	c.856A>G	p.Thr286Ala	missense_variant	Exon 8 of 11	ENST00000296591.10	NP_005702.3
EDIL3	NM_001278642.1	c.826A>G	p.Thr276Ala	missense_variant	Exon 7 of 10		NP_001265571.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EDIL3	ENST00000296591.10	c.856A>G	p.Thr286Ala	missense_variant	Exon 8 of 11	1	NM_005711.5	ENSP00000296591.4
EDIL3	ENST00000380138.3	c.826A>G	p.Thr276Ala	missense_variant	Exon 7 of 10	1		ENSP00000369483.3
EDIL3	ENST00000510271.1	n.405A>G		non_coding_transcript_exon_variant	Exon 3 of 5	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461582 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 727082

African (AFR) AF: 0.00 AC: 0 AN: 33470

American (AMR) AF: 0.00 AC: 0 AN: 44704

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26126

East Asian (EAS) AF: 0.00 AC: 0 AN: 39684

South Asian (SAS) AF: 0.00 AC: 0 AN: 86214

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53414

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5766

European-Non Finnish (NFE) AF: 8.99e-7 AC: 1 AN: 1111820

Other (OTH) AF: 0.00 AC: 0 AN: 60384

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.082
BayesDel_addAF	Pathogenic	0.35	D
BayesDel_noAF	Pathogenic	0.27
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.54	D;.
Eigen	Benign	-0.019
Eigen_PC	Benign	0.20
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.61	T;T
M_CAP	Uncertain	0.23	D
MetaRNN	Uncertain	0.62	D;D
MetaSVM	Uncertain	0.61	D
MutationAssessor	Benign	0.55	N;.
PhyloP100		7.6
PrimateAI	Uncertain	0.66	T
PROVEAN	Benign	-0.97	N;N
REVEL	Uncertain	0.59
Sift	Benign	0.077	T;T
Sift4G	Benign	0.21	T;T
Polyphen		0.045	B;B
Vest4		0.68
MutPred		0.50		Loss of methylation at K290 (P = 0.1354);.;
MVP		0.96
MPC		0.30
ClinPred		0.85	D
GERP RS		5.5
Varity_R		0.21
gMVP		0.39
Mutation Taster		=15/85	disease causing

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: rs201386908; hg19: chr5-83360615;