chr5-84060294-C-T
Position:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_005711.5(EDIL3):c.1137+6G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000682 in 1,612,276 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000067 ( 1 hom. )
Consequence
EDIL3
NM_005711.5 splice_donor_region, intron
NM_005711.5 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00007588
2
Clinical Significance
Conservation
PhyloP100: -1.73
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 5-84060294-C-T is Benign according to our data. Variant chr5-84060294-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 737422.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDIL3 | NM_005711.5 | c.1137+6G>A | splice_donor_region_variant, intron_variant | ENST00000296591.10 | |||
EDIL3 | NM_001278642.1 | c.1107+6G>A | splice_donor_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDIL3 | ENST00000296591.10 | c.1137+6G>A | splice_donor_region_variant, intron_variant | 1 | NM_005711.5 | P1 | |||
EDIL3 | ENST00000380138.3 | c.1107+6G>A | splice_donor_region_variant, intron_variant | 1 | |||||
EDIL3 | ENST00000510271.1 | n.686+6G>A | splice_donor_region_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152150Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
12
AN:
152150
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000292 AC: 73AN: 250150Hom.: 0 AF XY: 0.000288 AC XY: 39AN XY: 135222
GnomAD3 exomes
AF:
AC:
73
AN:
250150
Hom.:
AF XY:
AC XY:
39
AN XY:
135222
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000671 AC: 98AN: 1460010Hom.: 1 Cov.: 30 AF XY: 0.0000661 AC XY: 48AN XY: 726212
GnomAD4 exome
AF:
AC:
98
AN:
1460010
Hom.:
Cov.:
30
AF XY:
AC XY:
48
AN XY:
726212
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74446
GnomAD4 genome
AF:
AC:
12
AN:
152266
Hom.:
Cov.:
32
AF XY:
AC XY:
8
AN XY:
74446
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
Asia WGS
AF:
AC:
6
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at