6-165301952-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144980.4(C6orf118):c.370C>A(p.Gln124Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,666 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_144980.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C6orf118 | NM_144980.4 | c.370C>A | p.Gln124Lys | missense_variant | 2/9 | ENST00000230301.9 | NP_659417.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C6orf118 | ENST00000230301.9 | c.370C>A | p.Gln124Lys | missense_variant | 2/9 | 1 | NM_144980.4 | ENSP00000230301 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152070Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461596Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 727104
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152070Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 14, 2021 | The c.370C>A (p.Q124K) alteration is located in exon 2 (coding exon 2) of the C6orf118 gene. This alteration results from a C to A substitution at nucleotide position 370, causing the glutamine (Q) at amino acid position 124 to be replaced by a lysine (K). 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