10-11462884-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014688.5(USP6NL):āc.2044G>Cā(p.Glu682Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,594 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 (ā ).
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.2044G>C | p.Glu682Gln | 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.2044G>C | p.Glu682Gln | missense_variant | 15/15 | 1 | NM_014688.5 | ENSP00000476462 | P1 | |
USP6NL | ENST00000379237.6 | c.2113G>C | p.Glu705Gln | missense_variant | 14/14 | 5 | ENSP00000368539 | |||
USP6NL | ENST00000277575.5 | c.2095G>C | p.Glu699Gln | missense_variant | 14/14 | 5 | ENSP00000277575 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000282 AC: 7AN: 248354Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134818
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461460Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 726996
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | The c.2095G>C (p.E699Q) alteration is located in exon 14 (coding exon 14) of the USP6NL gene. This alteration results from a G to C substitution at nucleotide position 2095, causing the glutamic acid (E) at amino acid position 699 to be replaced by a glutamine (Q). 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