Variant rs56157240 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_199425.3(VSX1):c.711T>A(p.Pro237Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 1,613,902 control chromosomes in the GnomAD database, including 51,885 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 0.29 ( 7409 hom., cov: 31)

Exomes 𝑓: 0.24 ( 44476 hom. )

Consequence

VSX1
NM_199425.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.354

Variant links:

Genes affected

VSX1 (HGNC:12723): (visual system homeobox 1) The protein encoded by this gene contains a paired-like homeodomain and binds to the core of the locus control region of the red/green visual pigment gene cluster. The encoded protein may regulate expression of the cone opsin genes early in development. Mutations in this gene can cause posterior polymorphous corneal dystrophy and keratoconus. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

VSX1 links:

VSX1 (HGNC:):

VSX1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP7

Synonymous conserved (PhyloP=-0.354 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VSX1	NM_014588.6 linkuse as main transcript	c.627+84T>A		intron_variant		ENST00000376709.9	NP_055403.2	Q9NZR4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VSX1	ENST00000376709.9 linkuse as main transcript	c.627+84T>A		intron_variant		1	NM_014588.6	ENSP00000365899.3		Q9NZR4-1

Frequencies

GnomAD3 genomes

AF:

0.291

AC:

44275

AN:

151916

Hom.:

7384

Cov.:

show subpopulations

Gnomad AFR

AF:

0.439

Gnomad AMI

AF:

0.228

Gnomad AMR

AF:

0.339

Gnomad ASJ

AF:

0.324

Gnomad EAS

AF:

0.0191

Gnomad SAS

AF:

0.300

Gnomad FIN

AF:

0.203

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.225

Gnomad OTH

AF:

0.286

GnomAD3 exomes

AF:

0.259

AC:

65098

AN:

251466

Hom.:

10153

AF XY:

0.252

AC XY:

34233

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.449

Gnomad AMR exome

AF:

0.429

Gnomad ASJ exome

AF:

0.313

Gnomad EAS exome

AF:

0.0129

Gnomad SAS exome

AF:

0.288

Gnomad FIN exome

AF:

0.194

Gnomad NFE exome

AF:

0.220

Gnomad OTH exome

AF:

0.249

GnomAD4 exome

AF:

0.237

AC:

347089

AN:

1461868

Hom.:

44476

Cov.:

AF XY:

0.237

AC XY:

172565

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.452

Gnomad4 AMR exome

AF:

0.412

Gnomad4 ASJ exome

AF:

0.315

Gnomad4 EAS exome

AF:

0.00892

Gnomad4 SAS exome

AF:

0.289

Gnomad4 FIN exome

AF:

0.192

Gnomad4 NFE exome

AF:

0.228

Gnomad4 OTH exome

AF:

0.242

GnomAD4 genome

AF:

0.292

AC:

44349

AN:

152034

Hom.:

7409

Cov.:

AF XY:

0.288

AC XY:

21438

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.439

Gnomad4 AMR

AF:

0.340

Gnomad4 ASJ

AF:

0.324

Gnomad4 EAS

AF:

0.0184

Gnomad4 SAS

AF:

0.300

Gnomad4 FIN

AF:

0.203

Gnomad4 NFE

AF:

0.225

Gnomad4 OTH

AF:

0.282

Alfa

AF:

0.254

Hom.:

1786

Bravo

AF:

0.308

Asia WGS

AF:

0.163

AC:

568

AN:

3478

EpiCase

AF:

0.233

EpiControl

AF:

0.237

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.3

DANN

Benign

0.53

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over