rs2301092

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005711.5(EDIL3):​c.652-687C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,054 control chromosomes in the GnomAD database, including 1,316 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 1316 hom., cov: 32)

Consequence

EDIL3
NM_005711.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.206
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EDIL3NM_005711.5 linkuse as main transcriptc.652-687C>T intron_variant ENST00000296591.10
EDIL3NM_001278642.1 linkuse as main transcriptc.622-687C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EDIL3ENST00000296591.10 linkuse as main transcriptc.652-687C>T intron_variant 1 NM_005711.5 P1O43854-1
EDIL3ENST00000380138.3 linkuse as main transcriptc.622-687C>T intron_variant 1 O43854-2
EDIL3ENST00000510271.1 linkuse as main transcriptn.201-687C>T intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.109
AC:
16520
AN:
151936
Hom.:
1313
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.221
Gnomad AMI
AF:
0.0659
Gnomad AMR
AF:
0.0773
Gnomad ASJ
AF:
0.0678
Gnomad EAS
AF:
0.141
Gnomad SAS
AF:
0.138
Gnomad FIN
AF:
0.0319
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.0583
Gnomad OTH
AF:
0.0975
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.109
AC:
16544
AN:
152054
Hom.:
1316
Cov.:
32
AF XY:
0.108
AC XY:
7993
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.221
Gnomad4 AMR
AF:
0.0771
Gnomad4 ASJ
AF:
0.0678
Gnomad4 EAS
AF:
0.141
Gnomad4 SAS
AF:
0.137
Gnomad4 FIN
AF:
0.0319
Gnomad4 NFE
AF:
0.0583
Gnomad4 OTH
AF:
0.0965
Alfa
AF:
0.0748
Hom.:
235
Bravo
AF:
0.116
Asia WGS
AF:
0.130
AC:
452
AN:
3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.0
DANN
Benign
0.47

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2301092; hg19: chr5-83363112; API