Variant rs4710257 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001142800.2(EYS):c.8071+84T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 1,277,418 control chromosomes in the GnomAD database, including 68,460 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 6424 hom., cov: 32)

Exomes 𝑓: 0.33 ( 62036 hom. )

Consequence

EYS
NM_001142800.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.544

Variant links:

Genes affected

EYS (HGNC:21555): (eyes shut homolog) The product of this gene contains multiple epidermal growth factor (EGF)-like and LamG domains. The protein is expressed in the photoreceptor layer of the retina, and the gene is mutated in autosomal recessive retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

EYS links:

PHF3 (HGNC:8921): (PHD finger protein 3) This gene encodes a member of a PHD finger-containing gene family. This gene may function as a transcription factor and may be involved in glioblastomas development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

PHF3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 6-63762377-A-C is Benign according to our data. Variant chr6-63762377-A-C is described in ClinVar as [Benign]. Clinvar id is 1246986.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EYS	NM_001142800.2 linkuse as main transcript	c.8071+84T>G		intron_variant		ENST00000503581.6
EYS	NM_001292009.2 linkuse as main transcript	c.8071+84T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
EYS	ENST00000503581.6 linkuse as main transcript	c.8071+84T>G	intron_variant	5	NM_001142800.2	A2	Q5T1H1-1
EYS	ENST00000370621.7 linkuse as main transcript	c.8071+84T>G	intron_variant	1		P2	Q5T1H1-3
EYS	ENST00000398580.3 linkuse as main transcript	c.1385+84T>G	intron_variant	5
PHF3	ENST00000505138.1 linkuse as main transcript	c.364-15689A>C	intron_variant	3

Frequencies

GnomAD3 genomes

AF:

0.285

AC:

43220

AN:

151886

Hom.:

6419

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.352

Gnomad AMR

AF:

0.363

Gnomad ASJ

AF:

0.302

Gnomad EAS

AF:

0.284

Gnomad SAS

AF:

0.323

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.327

Gnomad OTH

AF:

0.308

GnomAD4 exome

AF:

0.328

AC:

369555

AN:

1125414

Hom.:

62036

AF XY:

0.329

AC XY:

185481

AN XY:

563962

show subpopulations

Gnomad4 AFR exome

AF:

0.191

Gnomad4 AMR exome

AF:

0.399

Gnomad4 ASJ exome

AF:

0.296

Gnomad4 EAS exome

AF:

0.244

Gnomad4 SAS exome

AF:

0.339

Gnomad4 FIN exome

AF:

0.232

Gnomad4 NFE exome

AF:

0.339

Gnomad4 OTH exome

AF:

0.328

GnomAD4 genome

AF:

0.284

AC:

43233

AN:

152004

Hom.:

6424

Cov.:

AF XY:

0.283

AC XY:

21012

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.193

Gnomad4 AMR

AF:

0.363

Gnomad4 ASJ

AF:

0.302

Gnomad4 EAS

AF:

0.283

Gnomad4 SAS

AF:

0.324

Gnomad4 FIN

AF:

0.219

Gnomad4 NFE

AF:

0.327

Gnomad4 OTH

AF:

0.305

Alfa

AF:

0.292

Hom.:

837

Bravo

AF:

0.293

Asia WGS

AF:

0.279

AC:

968

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.9

DANN

Benign

0.81

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over