X-17375904-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001291867.2(NHS):c.147C>T(p.Val49Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 23)
Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control
Consequence
NHS
NM_001291867.2 synonymous
NM_001291867.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0450
Publications
0 publications found
Genes affected
NHS (HGNC:7820): (NHS actin remodeling regulator) This gene encodes a protein containing four conserved nuclear localization signals. The encoded protein functions in eye, tooth, craniofacial and brain development, and it can regulate actin remodeling and cell morphology. Mutations in this gene have been shown to cause Nance-Horan syndrome, and also X-linked cataract-40. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, May 2014]
NHS Gene-Disease associations (from GenCC):
- Nance-Horan syndromeInheritance: XL Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: ClinGen, Orphanet, G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
- early-onset nuclear cataractInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP7
Synonymous conserved (PhyloP=-0.045 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 genomes
Cov.:
23
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 984560Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 315912
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
984560
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
315912
African (AFR)
AF:
AC:
0
AN:
20609
American (AMR)
AF:
AC:
0
AN:
19591
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
15904
East Asian (EAS)
AF:
AC:
0
AN:
22700
South Asian (SAS)
AF:
AC:
0
AN:
42496
European-Finnish (FIN)
AF:
AC:
0
AN:
24783
Middle Eastern (MID)
AF:
AC:
0
AN:
2666
European-Non Finnish (NFE)
AF:
AC:
0
AN:
794455
Other (OTH)
AF:
AC:
0
AN:
41356
GnomAD4 genome Cov.: 23
GnomAD4 genome
Cov.:
23
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Jun 01, 2015
Eurofins Ntd Llc (ga)
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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