chr10-119030064-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_199461.4(NANOS1):c.263A>C(p.His88Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H88N) has been classified 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NANOS1 | NM_199461.4 | c.263A>C | p.His88Pro | missense_variant | 1/1 | ENST00000425699.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NANOS1 | ENST00000425699.3 | c.263A>C | p.His88Pro | missense_variant | 1/1 | NM_199461.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 6AN: 147566Hom.: 0 Cov.: 32 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000224 AC: 26AN: 1160796Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 14AN XY: 563758
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000406 AC: 6AN: 147686Hom.: 0 Cov.: 32 AF XY: 0.0000417 AC XY: 3AN XY: 72012
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2021 | The c.263A>C (p.H88P) alteration is located in exon 1 (coding exon 1) of the NANOS1 gene. This alteration results from a A to C substitution at nucleotide position 263, causing the histidine (H) at amino acid position 88 to be replaced by a proline (P). 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