NM_017838.4:c.160+11C>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_017838.4(NHP2):c.160+11C>A variant causes a intron 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 Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Consequence
NHP2
NM_017838.4 intron
NM_017838.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.91
Publications
0 publications found
Genes affected
NHP2 (HGNC:14377): (NHP2 ribonucleoprotein) This gene is a member of the H/ACA snoRNPs (small nucleolar ribonucleoproteins) gene family. snoRNPs are involved in various aspects of rRNA processing and modification and have been classified into two families: C/D and H/ACA. The H/ACA snoRNPs also include the DKC1, NOLA1 and NOLA3 proteins. These four H/ACA snoRNP proteins localize to the dense fibrillar components of nucleoli and to coiled (Cajal) bodies in the nucleus. Both 18S rRNA production and rRNA pseudouridylation are impaired if any one of the four proteins is depleted. The four H/ACA snoRNP proteins are also components of the telomerase complex. This gene encodes a protein related to Saccharomyces cerevisiae Nhp2p. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2008]
NHP2 Gene-Disease associations (from GenCC):
- dyskeratosis congenita, autosomal recessive 2Inheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- dyskeratosis congenitaInheritance: AD, AR Classification: SUPPORTIVE, LIMITED Submitted by: Orphanet, ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -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 5-178153647-G-T is Benign according to our data. Variant chr5-178153647-G-T is described in CliVar as Likely_benign. Clinvar id is 1540602.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-178153647-G-T is described in CliVar as Likely_benign. Clinvar id is 1540602.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-178153647-G-T is described in CliVar as Likely_benign. Clinvar id is 1540602.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-178153647-G-T is described in CliVar as Likely_benign. Clinvar id is 1540602.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-178153647-G-T is described in CliVar as Likely_benign. Clinvar id is 1540602.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-178153647-G-T is described in CliVar as Likely_benign. Clinvar id is 1540602.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-178153647-G-T is described in CliVar as Likely_benign. Clinvar id is 1540602.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-178153647-G-T is described in CliVar as Likely_benign. Clinvar id is 1540602.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-178153647-G-T is described in CliVar as Likely_benign. Clinvar id is 1540602.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-178153647-G-T is described in CliVar as Likely_benign. Clinvar id is 1540602.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NHP2 | NM_017838.4 | c.160+11C>A | intron_variant | Intron 1 of 3 | ENST00000274606.8 | NP_060308.1 | ||
NHP2 | NM_001396110.1 | c.160+11C>A | intron_variant | Intron 1 of 4 | NP_001383039.1 | |||
NHP2 | NM_001034833.2 | c.160+11C>A | intron_variant | Intron 1 of 2 | NP_001030005.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Dyskeratosis congenita Benign:1
Jul 12, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
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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