chr10-119029991-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_199461.4(NANOS1):c.190G>A(p.Gly64Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000657 in 1,415,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_199461.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NANOS1 | NM_199461.4 | c.190G>A | p.Gly64Ser | missense_variant | 1/1 | ENST00000425699.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NANOS1 | ENST00000425699.3 | c.190G>A | p.Gly64Ser | missense_variant | 1/1 | NM_199461.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000464 AC: 7AN: 150928Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000105 AC: 6AN: 57218Hom.: 0 AF XY: 0.0000896 AC XY: 3AN XY: 33478
GnomAD4 exome AF: 0.0000680 AC: 86AN: 1264202Hom.: 0 Cov.: 32 AF XY: 0.0000660 AC XY: 41AN XY: 621594
GnomAD4 genome ? AF: 0.0000464 AC: 7AN: 150928Hom.: 0 Cov.: 32 AF XY: 0.0000407 AC XY: 3AN XY: 73688
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2022 | The c.190G>A (p.G64S) alteration is located in exon 1 (coding exon 1) of the NANOS1 gene. This alteration results from a G to A substitution at nucleotide position 190, causing the glycine (G) at amino acid position 64 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at