7-142863997-G-C

Position:

• chr7-142863997-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_004445.6(EPHB6):​c.197G>C​(p.Arg66Pro) 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. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency: Genomes: not found (cov: 34)
• Consequence: EPHB6 NM_004445.6 missense
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 1.85

Genes affected

EPHB6 (HGNC:3396): (EPH receptor B6) This gene encodes a member of a family of transmembrane proteins that function as receptors for ephrin-B family proteins. Unlike other members of this family, the encoded protein does not contain a functional kinase domain. Activity of this protein can influence cell adhesion and migration. Expression of this gene is downregulated during tumor progression, suggesting that the protein may suppress tumor invasion and metastasis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2867859).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPHB6	NM_004445.6	c.197G>C	p.Arg66Pro	missense_variant	Exon 7 of 20	ENST00000652003.1	NP_004436.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPHB6	ENST00000652003.1	c.197G>C	p.Arg66Pro	missense_variant	Exon 7 of 20		NM_004445.6	ENSP00000498670.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 107

GnomAD4 genome Cov.: 34

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Myoepithelial tumor Uncertain:1

Uncertain significance, no assertion criteria provided

research

Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine

Nov 01, 2022

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.069	T
BayesDel_noAF	Benign	-0.34
CADD	Benign	21
DANN	Uncertain	1.0
DEOGEN2	Benign	0.012	T;T
Eigen	Benign	0.042
Eigen_PC	Benign	0.085
FATHMM_MKL	Benign	0.74	D
LIST_S2	Uncertain	0.87	.;D
M_CAP	Benign	0.010	T
MetaRNN	Benign	0.29	T;T
MetaSVM	Benign	-0.91	T
PrimateAI	Benign	0.47	T
PROVEAN	Benign	-1.9	.;N
Sift	Benign	0.15	.;T
Sift4G	Benign	0.27	T;T
Vest4		0.48
MutPred		0.41		Loss of catalytic residue at R66 (P = 0.0651);Loss of catalytic residue at R66 (P = 0.0651);
MVP		0.71
ClinPred		0.79	D
GERP RS		3.3
gMVP		0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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.

Other links and lift over

hg19: chr7-142561755;