X-41473479-C-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_001378477.3(NYX):​c.23-12C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000116 in 858,707 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 23)
Exomes 𝑓: 0.0000012 ( 0 hom. 0 hem. )

Consequence

NYX
NM_001378477.3 intron

Scores

2
Splicing: ADA: 0.0006662
2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.153
Variant links:
Genes affected
NYX (HGNC:8082): (nyctalopin) The product of this gene belongs to the small leucine-rich proteoglycan (SLRP) family of proteins. Defects in this gene are the cause of congenital stationary night blindness type 1 (CSNB1), also called X-linked congenital stationary night blindness (XLCSNB). CSNB1 is a rare inherited retinal disorder characterized by impaired scotopic vision, myopia, hyperopia, nystagmus and reduced visual acuity. The role of other SLRP proteins suggests that mutations in this gene disrupt developing retinal interconnections involving the ON-bipolar cells, leading to the visual losses seen in patients with complete CSNB. [provided by RefSeq, Oct 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant X-41473479-C-G is Benign according to our data. Variant chrX-41473479-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 1672638.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NYXNM_001378477.3 linkc.23-12C>G intron_variant Intron 2 of 2 ENST00000378220.3 NP_001365406.2
NYXNM_022567.3 linkc.23-12C>G intron_variant Intron 1 of 1 NP_072089.2 Q9GZU5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NYXENST00000378220.3 linkc.23-12C>G intron_variant Intron 2 of 2 1 NM_001378477.3 ENSP00000367465.2 Q9GZU5
NYXENST00000342595.3 linkc.23-12C>G intron_variant Intron 1 of 1 1 ENSP00000340328.3 Q9GZU5
NYXENST00000486842.1 linkn.276-12C>G intron_variant Intron 1 of 1 3

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD4 exome
AF:
0.00000116
AC:
1
AN:
858707
Hom.:
0
Cov.:
28
AF XY:
0.00
AC XY:
0
AN XY:
259429
show subpopulations
Gnomad4 AFR exome
AF:
0.0000577
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
23
Bravo
AF:
0.0000151

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
May 16, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
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
BayesDel_noAF
Benign
-0.83
CADD
Benign
5.5
DANN
Benign
0.46

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.00067
dbscSNV1_RF
Benign
0.072
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: rs1355344476; hg19: chrX-41332732; API