20-47051863-A-G

Variant names:

• chr20-47051863-A-G
• rs878131
• NM_005244.5:c.416-20322A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005244.5(EYA2):​c.416-20322A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,108 control chromosomes in the GnomAD database, including 39,428 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 0.72 (39428 hom., cov: 32)
• Consequence: EYA2 NM_005244.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005244.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EYA2	NM_005244.5	MANE Select	c.416-20322A>G		intron	N/A	NP_005235.3
	EYA2	NM_172110.4		c.416-20322A>G		intron	N/A	NP_742108.2	O00167-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EYA2	ENST00000327619.10	TSL:2 MANE Select	c.416-20322A>G		intron	N/A	ENSP00000333640.5	O00167-1
	EYA2	ENST00000317304.10	TSL:1	c.416-20322A>G		intron	N/A	ENSP00000321590.6	E7ETN2
	EYA2	ENST00000357410.7	TSL:1	c.416-20322A>G		intron	N/A	ENSP00000349986.3	O00167-3

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109138 AN: 151990 Hom.: 39383 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.718 AC: 109250 AN: 152108 Hom.: 39428 Cov.: 32 AF XY: 0.718 AC XY: 53366 AN XY: 74346

African (AFR) AF: 0.750 AC: 31113 AN: 41478

American (AMR) AF: 0.642 AC: 9816 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2205 AN: 3472

East Asian (EAS) AF: 0.713 AC: 3687 AN: 5170

South Asian (SAS) AF: 0.655 AC: 3154 AN: 4814

European-Finnish (FIN) AF: 0.764 AC: 8089 AN: 10582

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.721 AC: 49009 AN: 67984

Other (OTH) AF: 0.687 AC: 1452 AN: 2114

Alfa AF: 0.721 Hom.: 58816

Bravo AF: 0.708

Asia WGS AF: 0.665 AC: 2315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.8
DANN	Benign	0.33
PhyloP100		0.10
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs878131; hg19: chr20-45680502;