10-11463172-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014688.5(USP6NL):c.1756C>T(p.Pro586Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,461,502 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014688.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USP6NL | NM_014688.5 | c.1756C>T | p.Pro586Ser | missense_variant | 15/15 | ENST00000609104.6 | NP_055503.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USP6NL | ENST00000609104.6 | c.1756C>T | p.Pro586Ser | missense_variant | 15/15 | 1 | NM_014688.5 | ENSP00000476462 | P1 | |
USP6NL | ENST00000379237.6 | c.1825C>T | p.Pro609Ser | missense_variant | 14/14 | 5 | ENSP00000368539 | |||
USP6NL | ENST00000277575.5 | c.1807C>T | p.Pro603Ser | missense_variant | 14/14 | 5 | ENSP00000277575 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 152198Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248582Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134928
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461502Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727030
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 03, 2022 | The c.1807C>T (p.P603S) alteration is located in exon 14 (coding exon 14) of the USP6NL gene. This alteration results from a C to T substitution at nucleotide position 1807, causing the proline (P) at amino acid position 603 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