rs79587607

Variant summary

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

The NM_005232.5(EPHA1):​c.71G>C​(p.Arg24Pro) variant causes a missense 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. 14/21 in silico tools predict 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: 26)

Consequence

EPHA1
NM_005232.5 missense

Scores

1
1
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.452
Variant links:
Genes affected
EPHA1 (HGNC:3385): (EPH receptor A1) This gene belongs to the ephrin receptor subfamily of the protein-tyrosine kinase family. EPH and EPH-related receptors have been implicated in mediating developmental events, particularly in the nervous system. Receptors in the EPH subfamily typically have a single kinase domain and an extracellular region containing a Cys-rich domain and 2 fibronectin type III repeats. The ephrin receptors are divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. This gene is expressed in some human cancer cell lines and has been implicated in carcinogenesis. [provided by RefSeq, Jul 2008]
EPHA1-AS1 (HGNC:27799): (EPHA1 antisense RNA 1)

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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=0.110049725).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EPHA1NM_005232.5 linkc.71G>C p.Arg24Pro missense_variant Exon 1 of 18 ENST00000275815.4 NP_005223.4 P21709-1
EPHA1-AS1NR_033897.1 linkn.74+849C>G intron_variant Intron 1 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EPHA1ENST00000275815.4 linkc.71G>C p.Arg24Pro missense_variant Exon 1 of 18 1 NM_005232.5 ENSP00000275815.3 P21709-1

Frequencies

GnomAD3 genomes
Cov.:
26
GnomAD4 exome
Cov.:
11
GnomAD4 genome
Cov.:
26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.069
BayesDel_addAF
Benign
-0.092
T
BayesDel_noAF
Benign
-0.37
CADD
Benign
19
DANN
Benign
0.78
DEOGEN2
Benign
0.028
T
Eigen
Benign
-0.71
Eigen_PC
Benign
-0.53
FATHMM_MKL
Benign
0.17
N
M_CAP
Uncertain
0.18
D
MetaRNN
Benign
0.11
T
MetaSVM
Benign
-0.96
T
MutationAssessor
Benign
-0.69
N
PrimateAI
Pathogenic
0.81
D
PROVEAN
Benign
1.0
N
REVEL
Benign
0.14
Sift
Benign
0.51
T
Sift4G
Benign
0.34
T
Polyphen
0.0010
B
Vest4
0.18
MutPred
0.40
Gain of glycosylation at R24 (P = 0.0245);
MVP
0.58
MPC
0.20
ClinPred
0.23
T
GERP RS
2.8
Varity_R
0.15
gMVP
0.36

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs79587607; hg19: chr7-143105828; API