rs7256163

chr19-6958123-A-Gchr19-6958123-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_024075.2(ADGRE4P):n.1694-899T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,932 control chromosomes in the GnomAD database, including 10,919 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 0.36 (10919 hom., cov: 31)
• Consequence: ADGRE4P NR_024075.2 intron, non_coding_transcript
• 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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADGRE4P	NR_024075.2	n.1694-899T>C		intron_variant, non_coding_transcript_variant
ADGRE4P	NR_174976.1	n.2138-899T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADGRE4P	ENST00000597372.2	n.1589-899T>C		intron_variant, non_coding_transcript_variant
	ENST00000600751.6	n.1715-899T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000639977.1	n.2155-899T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000640515.1	n.2205-899T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54608 AN: 151814 Hom.: 10911 Cov.: 31

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0921

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.360 AC: 54659 AN: 151932 Hom.: 10919 Cov.: 31 AF XY: 0.352 AC XY: 26126 AN XY: 74264

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.0917

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.353

Alfa AF: 0.323 Hom.: 11508

Bravo AF: 0.372

Asia WGS AF: 0.185 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.4
Dann	Benign	0.80

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;