10-119030300-CCCGCCGCCGCCG-CCCGCCG
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2
The NM_199461.4(NANOS1):c.514_519del(p.Ala172_Ala173del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000312 in 1,153,950 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000047 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000029 ( 0 hom. )
Consequence
NANOS1
NM_199461.4 inframe_deletion
NM_199461.4 inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.46
Genes affected
NANOS1 (HGNC:23044): (nanos C2HC-type zinc finger 1) This gene encodes a CCHC-type zinc finger protein that is a member of the nanos family. This protein co-localizes with the RNA-binding protein pumilio RNA-binding family member 2 and may be involved in regulating translation as a post-transcriptional repressor. Mutations in this gene are associated with spermatogenic impairment. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_199461.4.
BS2
?
High AC in GnomAd at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NANOS1 | NM_199461.4 | c.514_519del | p.Ala172_Ala173del | inframe_deletion | 1/1 | ENST00000425699.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NANOS1 | ENST00000425699.3 | c.514_519del | p.Ala172_Ala173del | inframe_deletion | 1/1 | NM_199461.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000474 AC: 7AN: 147538Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00203 AC: 1AN: 492Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 272
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GnomAD4 exome AF: 0.0000288 AC: 29AN: 1006412Hom.: 0 AF XY: 0.0000274 AC XY: 13AN XY: 474800
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GnomAD4 genome ? AF: 0.0000474 AC: 7AN: 147538Hom.: 0 Cov.: 32 AF XY: 0.0000418 AC XY: 3AN XY: 71850
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at