Genetic Variant NM_078481.4:c.176C>A (chr19-14388804-C-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_078481.4(ADGRE5):c.176C>A(p.Thr59Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,451,284 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 28)

Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

ADGRE5
NM_078481.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -3.76

Variant links:

Genes affected

ADGRE5 (HGNC:1711): (adhesion G protein-coupled receptor E5) This gene encodes a member of the EGF-TM7 subfamily of adhesion G protein-coupled receptors, which mediate cell-cell interactions. These proteins are cleaved by self-catalytic proteolysis into a large extracellular subunit and seven-span transmembrane subunit, which associate at the cell surface as a receptor complex. The encoded protein may play a role in cell adhesion as well as leukocyte recruitment, activation and migration, and contains multiple extracellular EGF-like repeats which mediate binding to chondroitin sulfate and the cell surface complement regulatory protein CD55. Expression of this gene may play a role in the progression of several types of cancer. Alternatively spliced transcript variants encoding multiple isoforms with 3 to 5 EGF-like repeats have been observed for this gene. This gene is found in a cluster with other EGF-TM7 genes on the short arm of chromosome 19. [provided by RefSeq, Jun 2011]

ADGRE5 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.09031376).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRE5	NM_078481.4 link	c.176C>A	p.Thr59Lys	missense_variant	Exon 3 of 20	ENST00000242786.6	NP_510966.1	P48960-1
ADGRE5	NM_001025160.3 link	c.176C>A	p.Thr59Lys	missense_variant	Exon 3 of 19		NP_001020331.1	P48960-3
ADGRE5	NM_001784.6 link	c.176C>A	p.Thr59Lys	missense_variant	Exon 3 of 18		NP_001775.2	P48960-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRE5	ENST00000242786.6 link	c.176C>A	p.Thr59Lys	missense_variant	Exon 3 of 20	1	NM_078481.4	ENSP00000242786.4		P48960-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.89e-7

AC:

AN:

1451284

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

722230

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

9.06e-7

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Oct 12, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.176C>A (p.T59K) alteration is located in exon 3 (coding exon 3) of the ADGRE5 gene. This alteration results from a C to A substitution at nucleotide position 176, causing the threonine (T) at amino acid position 59 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.089

BayesDel_addAF

Benign

-0.15

BayesDel_noAF

Benign

-0.46

CADD

Benign

0.0020

DANN

Benign

0.61

DEOGEN2

Benign

0.021

.;T;T;.;T;.

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.0075

LIST_S2

Benign

0.044

T;T;T;T;T;T

M_CAP

Benign

0.056

MetaRNN

Benign

0.090

T;T;T;T;T;T

MetaSVM

Benign

-0.97

PrimateAI

Benign

0.31

PROVEAN

Benign

-1.3

N;.;.;N;.;N

REVEL

Benign

0.12

Sift

Benign

0.90

T;.;.;T;.;T

Sift4G

Benign

0.92

T;T;T;T;T;T

Vest4

0.22

MutPred

0.40

Gain of ubiquitination at T59 (P = 0.0117);Gain of ubiquitination at T59 (P = 0.0117);.;Gain of ubiquitination at T59 (P = 0.0117);Gain of ubiquitination at T59 (P = 0.0117);Gain of ubiquitination at T59 (P = 0.0117);

MVP

0.088

MPC

0.67

ClinPred

0.15

GERP RS

-6.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

gMVP

0.80

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over