10-119030300-CCCGCCGCCGCCG-CCCGCCGCCGCCGCCGCCGCCG
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2
The NM_199461.4(NANOS1):c.511_519dup(p.Ala171_Ala173dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,154,096 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 0.00010 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000015 ( 0 hom. )
Consequence
NANOS1
NM_199461.4 inframe_insertion
NM_199461.4 inframe_insertion
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]
Genome browser will be placed here
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 15 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NANOS1 | NM_199461.4 | c.511_519dup | p.Ala171_Ala173dup | inframe_insertion | 1/1 | ENST00000425699.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NANOS1 | ENST00000425699.3 | c.511_519dup | p.Ala171_Ala173dup | inframe_insertion | 1/1 | NM_199461.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000102 AC: 15AN: 147538Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
15
AN:
147538
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000149 AC: 15AN: 1006558Hom.: 0 Cov.: 32 AF XY: 0.0000105 AC XY: 5AN XY: 474868
GnomAD4 exome
AF:
AC:
15
AN:
1006558
Hom.:
Cov.:
32
AF XY:
AC XY:
5
AN XY:
474868
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000102 AC: 15AN: 147538Hom.: 0 Cov.: 32 AF XY: 0.0000974 AC XY: 7AN XY: 71850
GnomAD4 genome
?
AF:
AC:
15
AN:
147538
Hom.:
Cov.:
32
AF XY:
AC XY:
7
AN XY:
71850
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at