6-63814258-G-T

Variant names:

• chr6-63814258-G-T
• rs6921058
• NM_001142800.2:c.7229-7886C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142800.2(EYS):​c.7229-7886C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,978 control chromosomes in the GnomAD database, including 21,242 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 0.51 (21242 hom., cov: 32)
• Consequence: EYS NM_001142800.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

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]

SCAT8 (HGNC:40967): (S-phase cancer associated transcript 8)

ACMG classification

Verdict is Benign. Variant got -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 = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EYS	NM_001142800.2	c.7229-7886C>A		intron_variant	Intron 36 of 42	ENST00000503581.6	NP_001136272.1
EYS	NM_001292009.2	c.7229-7886C>A		intron_variant	Intron 36 of 43		NP_001278938.1
SCAT8	NR_157848.1	n.52-6982G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EYS	ENST00000503581.6	c.7229-7886C>A		intron_variant	Intron 36 of 42	5	NM_001142800.2	ENSP00000424243.1

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76857 AN: 151860 Hom.: 21193 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.506 AC: 76963 AN: 151978 Hom.: 21242 Cov.: 32 AF XY: 0.506 AC XY: 37608 AN XY: 74258

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.466

Alfa AF: 0.353 Hom.: 1249

Bravo AF: 0.531

Asia WGS AF: 0.462 AC: 1604 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.72
DANN	Benign	0.22

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

Other links and lift over

dbSNP: rs6921058; hg19: chr6-64524151;