rs587781103
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_001130969.3(NSMF):c.71+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00275 in 1,280,446 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0030 ( 4 hom. )
Consequence
NSMF
NM_001130969.3 intron
NM_001130969.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.456
Genes affected
NSMF (HGNC:29843): (NMDA receptor synaptonuclear signaling and neuronal migration factor) The protein encoded by this gene is involved in guidance of olfactory axon projections and migration of luteinizing hormone-releasing hormone neurons. Defects in this gene are a cause of idiopathic hypogonadotropic hypogonadism (IHH). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]
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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=-0.45).
BP6
?
Variant 9-137459023-C-T is Benign according to our data. Variant chr9-137459023-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 138563.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAd4 at 190 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NSMF | NM_001130969.3 | c.71+9G>A | intron_variant | ENST00000371475.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSMF | ENST00000371475.9 | c.71+9G>A | intron_variant | 1 | NM_001130969.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00125 AC: 190AN: 151918Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00221 AC: 17AN: 7698Hom.: 0 AF XY: 0.00108 AC XY: 5AN XY: 4620
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GnomAD4 exome AF: 0.00295 AC: 3331AN: 1128420Hom.: 4 Cov.: 30 AF XY: 0.00289 AC XY: 1561AN XY: 539712
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GnomAD4 genome ? AF: 0.00125 AC: 190AN: 152026Hom.: 0 Cov.: 33 AF XY: 0.00109 AC XY: 81AN XY: 74344
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 09, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 04, 2013 | This 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 provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 30, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at