chrX-17375203-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001291867.2(NHS):c.-555G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0221 in 111,683 control chromosomes in the GnomAD database, including 28 homozygotes. There are 711 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.022 ( 28 hom., 711 hem., cov: 23)
Consequence
NHS
NM_001291867.2 5_prime_UTR
NM_001291867.2 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.59
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant X-17375203-G-A is Benign according to our data. Variant chrX-17375203-G-A is described in ClinVar as [Benign]. Clinvar id is 1275467.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0221 (2467/111683) while in subpopulation NFE AF= 0.0327 (1726/52860). AF 95% confidence interval is 0.0314. There are 28 homozygotes in gnomad4. There are 711 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 28 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NHS | NM_001291867.2 | c.-555G>A | 5_prime_UTR_variant | 1/9 | ENST00000676302.1 | ||
NHS | NM_198270.4 | c.-555G>A | 5_prime_UTR_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHS | ENST00000676302.1 | c.-555G>A | 5_prime_UTR_variant | 1/9 | NM_001291867.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0221 AC: 2467AN: 111636Hom.: 28 Cov.: 23 AF XY: 0.0210 AC XY: 710AN XY: 33856
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0221 AC: 2467AN: 111683Hom.: 28 Cov.: 23 AF XY: 0.0210 AC XY: 711AN XY: 33913
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 11, 2018 | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at