rs75395981

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000261980.3(VSX2):​c.871G>A​(p.Asp291Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0132 in 1,593,940 control chromosomes in the GnomAD database, including 542 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. D291D) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.017 ( 82 hom., cov: 33)
Exomes 𝑓: 0.013 ( 460 hom. )

Consequence

VSX2
ENST00000261980.3 missense

Scores

2
16

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 6.91
Variant links:
Genes affected
VSX2 (HGNC:1975): (visual system homeobox 2) This gene encodes a homeobox protein originally described as a retina-specific transcription factor. Mutations in this gene are associated with microphthalmia, cataracts and iris abnormalities. [provided by RefSeq, Oct 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0015234649).
BP6
Variant 14-74260704-G-A is Benign according to our data. Variant chr14-74260704-G-A is described in ClinVar as [Benign]. Clinvar id is 197895.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-74260704-G-A is described in Lovd as [Likely_benign].
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0824 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
VSX2NM_182894.3 linkuse as main transcriptc.871G>A p.Asp291Asn missense_variant 5/5 ENST00000261980.3 NP_878314.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
VSX2ENST00000261980.3 linkuse as main transcriptc.871G>A p.Asp291Asn missense_variant 5/51 NM_182894.3 ENSP00000261980 P1

Frequencies

GnomAD3 genomes
AF:
0.0172
AC:
2617
AN:
152214
Hom.:
81
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00654
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0861
Gnomad ASJ
AF:
0.0213
Gnomad EAS
AF:
0.0276
Gnomad SAS
AF:
0.0331
Gnomad FIN
AF:
0.00574
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00810
Gnomad OTH
AF:
0.0191
GnomAD3 exomes
AF:
0.0303
AC:
6417
AN:
211694
Hom.:
322
AF XY:
0.0263
AC XY:
3006
AN XY:
114172
show subpopulations
Gnomad AFR exome
AF:
0.00642
Gnomad AMR exome
AF:
0.128
Gnomad ASJ exome
AF:
0.0228
Gnomad EAS exome
AF:
0.0274
Gnomad SAS exome
AF:
0.0281
Gnomad FIN exome
AF:
0.00651
Gnomad NFE exome
AF:
0.00882
Gnomad OTH exome
AF:
0.0227
GnomAD4 exome
AF:
0.0128
AC:
18381
AN:
1441608
Hom.:
460
Cov.:
31
AF XY:
0.0126
AC XY:
9021
AN XY:
714970
show subpopulations
Gnomad4 AFR exome
AF:
0.00554
Gnomad4 AMR exome
AF:
0.120
Gnomad4 ASJ exome
AF:
0.0243
Gnomad4 EAS exome
AF:
0.0237
Gnomad4 SAS exome
AF:
0.0259
Gnomad4 FIN exome
AF:
0.00641
Gnomad4 NFE exome
AF:
0.00747
Gnomad4 OTH exome
AF:
0.0154
GnomAD4 genome
AF:
0.0173
AC:
2635
AN:
152332
Hom.:
82
Cov.:
33
AF XY:
0.0189
AC XY:
1406
AN XY:
74490
show subpopulations
Gnomad4 AFR
AF:
0.00678
Gnomad4 AMR
AF:
0.0863
Gnomad4 ASJ
AF:
0.0213
Gnomad4 EAS
AF:
0.0276
Gnomad4 SAS
AF:
0.0335
Gnomad4 FIN
AF:
0.00574
Gnomad4 NFE
AF:
0.00810
Gnomad4 OTH
AF:
0.0194
Alfa
AF:
0.0120
Hom.:
65
Bravo
AF:
0.0233
TwinsUK
AF:
0.00620
AC:
23
ALSPAC
AF:
0.0112
AC:
43
ESP6500AA
AF:
0.00525
AC:
23
ESP6500EA
AF:
0.0107
AC:
92
ExAC
AF:
0.0221
AC:
2677
Asia WGS
AF:
0.0420
AC:
145
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Isolated microphthalmia 2 Benign:3
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 01, 2024- -
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 10, 2021- -
Microphthalmia, isolated, with coloboma 3 Benign:2
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 10, 2021- -
not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxMar 22, 2018This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Aug 29, 2014- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.079
BayesDel_addAF
Benign
-0.50
T
BayesDel_noAF
Benign
-0.38
CADD
Uncertain
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.37
T
Eigen
Benign
-0.065
Eigen_PC
Benign
0.10
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Benign
0.76
T
MetaRNN
Benign
0.0015
T
MetaSVM
Benign
-0.58
T
MutationAssessor
Benign
1.2
L
MutationTaster
Benign
1.0
D
PrimateAI
Benign
0.43
T
PROVEAN
Benign
-1.8
N
REVEL
Benign
0.26
Sift
Benign
0.035
D
Sift4G
Benign
0.24
T
Polyphen
0.13
B
Vest4
0.090
MPC
0.21
ClinPred
0.015
T
GERP RS
4.8
Varity_R
0.11
gMVP
0.21

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.

Other links and lift over

dbSNP: rs75395981; hg19: chr14-74727407; API