rs1367228
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001039348.3(EFEMP1):c.518-3571G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,014 control chromosomes in the GnomAD database, including 24,201 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 0.54 ( 24201 hom., cov: 32)
Consequence
EFEMP1
NM_001039348.3 intron
NM_001039348.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0640
Genes affected
EFEMP1 (HGNC:3218): (EGF containing fibulin extracellular matrix protein 1) This gene encodes a member of the fibulin family of extracellular matrix glycoproteins. Like all members of this family, the encoded protein contains tandemly repeated epidermal growth factor-like repeats followed by a C-terminus fibulin-type domain. This gene is upregulated in malignant gliomas and may play a role in the aggressive nature of these tumors. Mutations in this gene are associated with Doyne honeycomb retinal dystrophy. Alternatively spliced transcript variants that encode the same protein have been described.[provided by RefSeq, Nov 2009]
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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=-0.79).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFEMP1 | NM_001039348.3 | c.518-3571G>T | intron_variant | ENST00000355426.8 | |||
EFEMP1 | NM_001039349.3 | c.518-3571G>T | intron_variant | ||||
EFEMP1 | XM_005264205.5 | c.518-3571G>T | intron_variant | ||||
EFEMP1 | XM_017003586.3 | c.518-3571G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFEMP1 | ENST00000355426.8 | c.518-3571G>T | intron_variant | 1 | NM_001039348.3 | P1 | |||
EFEMP1 | ENST00000394555.6 | c.518-3571G>T | intron_variant | 1 | P1 | ||||
EFEMP1 | ENST00000634374.1 | c.117-3571G>T | intron_variant | 5 | |||||
EFEMP1 | ENST00000635671.1 | c.*410-3571G>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.544 AC: 82558AN: 151896Hom.: 24168 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.544 AC: 82642AN: 152014Hom.: 24201 Cov.: 32 AF XY: 0.546 AC XY: 40601AN XY: 74304
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2648
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at