20-47089302-A-G

Position:

• chr20-47089302-A-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005244.5(EYA2):​c.725A>G​(p.His242Arg) 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. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: EYA2 NM_005244.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.97

Genes affected

EYA2 (HGNC:3520): (EYA transcriptional coactivator and phosphatase 2) This gene encodes a member of the eyes absent (EYA) family of proteins. The encoded protein may be post-translationally modified and may play a role in eye development. A similar protein in mice can act as a transcriptional activator. Alternative splicing results in multiple transcript variants, but the full-length natures of all of these variants have not yet been determined. [provided by RefSeq, Jul 2009]

EYA2 (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 (MetaRNN=0.04219374).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EYA2	NM_005244.5	c.725A>G	p.His242Arg	missense_variant	8/16	ENST00000327619.10	NP_005235.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EYA2	ENST00000327619.10	c.725A>G	p.His242Arg	missense_variant	8/16	2	NM_005244.5	ENSP00000333640.5
EYA2	ENST00000497062.6	c.653A>G	p.His218Arg	missense_variant	8/16	1		ENSP00000417105.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 05, 2024

The c.725A>G (p.H242R) alteration is located in exon 8 (coding exon 7) of the EYA2 gene. This alteration results from a A to G substitution at nucleotide position 725, causing the histidine (H) at amino acid position 242 to be replaced by an arginine (R). 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	0.079
BayesDel_addAF	Benign	-0.015	T
BayesDel_noAF	Benign	-0.26
CADD	Benign	11
DANN	Benign	0.86
DEOGEN2	Benign	0.023	T;.;T;.;T;T
Eigen	Benign	-0.97
Eigen_PC	Benign	-0.81
FATHMM_MKL	Uncertain	0.77	D
LIST_S2	Benign	0.83	T;D;D;T;.;D
M_CAP	Benign	0.053	D
MetaRNN	Benign	0.042	T;T;T;T;T;T
MetaSVM	Benign	-0.50	T
MutationAssessor	Benign	-1.3	N;N;.;.;.;.
PrimateAI	Benign	0.42	T
PROVEAN	Benign	0.73	N;N;.;.;N;N
REVEL	Benign	0.18
Sift	Benign	1.0	T;T;.;.;T;T
Sift4G	Benign	0.68	T;T;T;T;T;T
Polyphen		0.0	B;B;B;.;B;.
Vest4		0.27
MutPred		0.15		Gain of MoRF binding (P = 0.0333);Gain of MoRF binding (P = 0.0333);Gain of MoRF binding (P = 0.0333);.;Gain of MoRF binding (P = 0.0333);.;
MVP		0.53
MPC		0.14
ClinPred		0.14	T
GERP RS		0.84
Varity_R		0.027
gMVP		0.39

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-45717941;