19-6958123-A-T

Variant names:

• chr19-6958123-A-T
• rs7256163
• ENST00000597372.2:n.1589-899T>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_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
• 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]

ENSG00000290427 (HGNC:):

ACMG classification

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

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRE4P	NR_024075.2	n.1694-899T>A		intron_variant	Intron 14 of 16
ADGRE4P	NR_174976.1	n.2138-899T>A		intron_variant	Intron 12 of 14

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

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7256163; hg19: chr19-6958134;