rs199553930

Variant names:

• chr5-84064829-T-A
• rs199553930
• NM_005711.5:c.823A>T

Your query was ambiguous. Multiple possible variants found:

• chr5-84064829-T-A
• chr5-84064829-T-C

Variant summary

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

The NM_005711.5(EDIL3):​c.823A>T​(p.Ile275Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000000686 in 1,458,518 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. I275V) has been classified as Likely benign.

• 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: 3.81
• 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.823A>T	p.Ile275Phe	missense_variant	Exon 8 of 11	ENST00000296591.10	NP_005702.3
EDIL3	NM_001278642.1	c.793A>T	p.Ile265Phe	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.823A>T	p.Ile275Phe	missense_variant	Exon 8 of 11	1	NM_005711.5	ENSP00000296591.4
EDIL3	ENST00000380138.3	c.793A>T	p.Ile265Phe	missense_variant	Exon 7 of 10	1		ENSP00000369483.3
EDIL3	ENST00000510271.1	n.372A>T		non_coding_transcript_exon_variant	Exon 3 of 5	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1458518 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 725356

African (AFR) AF: 0.00 AC: 0 AN: 33346

American (AMR) AF: 0.00 AC: 0 AN: 44066

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25994

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39654

South Asian (SAS) AF: 0.00 AC: 0 AN: 85374

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53382

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5746

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1110706

Other (OTH) AF: 0.00 AC: 0 AN: 60250

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.090
BayesDel_addAF	Uncertain	0.076	D
BayesDel_noAF	Benign	-0.13
CADD	Benign	21
DANN	Benign	0.58
DEOGEN2	Uncertain	0.60	D;.
Eigen	Benign	-0.47
Eigen_PC	Benign	-0.31
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Uncertain	0.93	D;D
M_CAP	Pathogenic	0.35	D
MetaRNN	Uncertain	0.53	D;D
MetaSVM	Pathogenic	0.79	D
MutationAssessor	Benign	0.81	L;.
PhyloP100		3.8
PrimateAI	Benign	0.31	T
PROVEAN	Benign	-1.4	N;N
REVEL	Uncertain	0.45
Sift	Benign	0.12	T;T
Sift4G	Benign	0.25	T;T
Polyphen		0.052	B;B
Vest4		0.23
MutPred		0.38		Gain of disorder (P = 0.1943);.;
MVP		0.95
MPC		0.44
ClinPred		0.63	D
GERP RS		4.6
Varity_R		0.16
gMVP		0.51
Mutation Taster		=70/30	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs199553930; hg19: chr5-83360648;