chr10-119030154-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBS2_Supporting
The NM_199461.4(NANOS1):c.353C>A(p.Ser118Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000597 in 1,357,714 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 -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NANOS1 | NM_199461.4 | c.353C>A | p.Ser118Tyr | missense_variant | 1/1 | ENST00000425699.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NANOS1 | ENST00000425699.3 | c.353C>A | p.Ser118Tyr | missense_variant | 1/1 | NM_199461.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000859 AC: 13AN: 151320Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000564 AC: 68AN: 1206394Hom.: 0 Cov.: 33 AF XY: 0.0000593 AC XY: 35AN XY: 590144
GnomAD4 genome AF: 0.0000859 AC: 13AN: 151320Hom.: 0 Cov.: 32 AF XY: 0.0000812 AC XY: 6AN XY: 73910
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2022 | The c.353C>A (p.S118Y) alteration is located in exon 1 (coding exon 1) of the NANOS1 gene. This alteration results from a C to A substitution at nucleotide position 353, causing the serine (S) at amino acid position 118 to be replaced by a tyrosine (Y). 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