19-6958123-A-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NR_024075.2(ADGRE4P):n.1694-899T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
Consequence
ADGRE4P
NR_024075.2 intron
NR_024075.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.416
Genes affected
ADGRE4P (HGNC:19240): (adhesion G protein-coupled receptor E4, pseudogene) This gene is a member of the EGF-TM7 receptor gene family which is thought to play a role in leukocyte adhesion and migration. In other vertebrates, including nonhuman primates, this gene encodes a protein containing N-terminal EGF domains and a C-terminal transmembrane domain. Sequence evidence for the human gene, however, indicates nucleotide deletion in the genomic sequence would result in frameshift and early termination of translation. A protein expressed by this gene would be soluble rather than expressed on the cell surface. As the encoded protein has not been detected, this gene may represent a transcribed pseudogene. [provided by RefSeq, Aug 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADGRE4P | ENST00000597372.2 | n.1589-899T>A | intron_variant | Intron 13 of 14 | 6 | |||||
ENSG00000290427 | ENST00000600751.6 | n.1715-899T>A | intron_variant | Intron 14 of 16 | 5 | |||||
ENSG00000290427 | ENST00000639977.1 | n.2155-899T>A | intron_variant | Intron 12 of 14 | 5 | |||||
ENSG00000290427 | ENST00000640515.1 | n.2205-899T>A | intron_variant | Intron 13 of 15 | 5 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at