rs571843718

Variant names:

• chr6-63720183-AT-A
• rs571843718
• NM_001142800.2:c.*412delA

Your query was ambiguous. Multiple possible variants found:

• chr6-63720183-AT-A
• chr6-63720183-AT-ATT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001142800.2(EYS):​c.*412delA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000941 in 222,122 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.00090 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0010 (0 hom.)
• Consequence: EYS NM_001142800.2 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.194
• Publications: 0 publications found

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]

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EYS	NM_001142800.2	c.*412delA		3_prime_UTR_variant	Exon 43 of 43	ENST00000503581.6	NP_001136272.1
PHF3	NM_001370348.2	c.*6482delT		3_prime_UTR_variant	Exon 16 of 16	ENST00000262043.8	NP_001357277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EYS	ENST00000503581.6	c.*412delA		3_prime_UTR_variant	Exon 43 of 43	5	NM_001142800.2	ENSP00000424243.1
PHF3	ENST00000262043.8	c.*6482delT		3_prime_UTR_variant	Exon 16 of 16	5	NM_001370348.2	ENSP00000262043.4
EYS	ENST00000370621.7	c.*412delA		3_prime_UTR_variant	Exon 44 of 44	1		ENSP00000359655.3
PHF3	ENST00000505138.1	c.361+8828delT		intron_variant	Intron 3 of 4	3		ENSP00000421417.1

Frequencies

GnomAD3 genomes AF: 0.000901 AC: 137 AN: 151972 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000290

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000566

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00171

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00103 AC: 72 AN: 70030 Hom.: 0 Cov.: 0 AF XY: 0.000840 AC XY: 29 AN XY: 34508

African (AFR) AF: 0.000316 AC: 1 AN: 3160

American (AMR) AF: 0.00 AC: 0 AN: 2172

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3254

East Asian (EAS) AF: 0.00 AC: 0 AN: 6056

South Asian (SAS) AF: 0.00 AC: 0 AN: 626

European-Finnish (FIN) AF: 0.000394 AC: 1 AN: 2536

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 384

European-Non Finnish (NFE) AF: 0.00136 AC: 63 AN: 46490

Other (OTH) AF: 0.00131 AC: 7 AN: 5352

GnomAD4 genome AF: 0.000901 AC: 137 AN: 152092 Hom.: 1 Cov.: 32 AF XY: 0.000901 AC XY: 67 AN XY: 74360

African (AFR) AF: 0.000289 AC: 12 AN: 41548

American (AMR) AF: 0.000131 AC: 2 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.00 AC: 0 AN: 4826

European-Finnish (FIN) AF: 0.000566 AC: 6 AN: 10606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00171 AC: 116 AN: 67900

Other (OTH) AF: 0.00 AC: 0 AN: 2106

Alfa AF: 0.000571 Hom.: 0

Bravo AF: 0.000820

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Retinitis Pigmentosa, Recessive Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.19

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: rs571843718; hg19: chr6-64430079;