rs13077498
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_198562.3(C3orf62):c.328G>A(p.Glu110Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 1,614,096 control chromosomes in the GnomAD database, including 8,566 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_198562.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C3orf62 | NM_198562.3 | c.328G>A | p.Glu110Lys | missense_variant | 1/3 | ENST00000343010.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C3orf62 | ENST00000343010.8 | c.328G>A | p.Glu110Lys | missense_variant | 1/3 | 1 | NM_198562.3 | P1 | |
C3orf62 | ENST00000436325.1 | c.322G>A | p.Glu108Lys | missense_variant | 2/4 | 4 | |||
C3orf62 | ENST00000424960.1 | c.267+31G>A | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0934 AC: 14200AN: 152110Hom.: 737 Cov.: 32
GnomAD3 exomes AF: 0.0880 AC: 22127AN: 251494Hom.: 1100 AF XY: 0.0873 AC XY: 11863AN XY: 135922
GnomAD4 exome AF: 0.101 AC: 147779AN: 1461868Hom.: 7829 Cov.: 32 AF XY: 0.0996 AC XY: 72423AN XY: 727234
GnomAD4 genome ? AF: 0.0933 AC: 14201AN: 152228Hom.: 737 Cov.: 32 AF XY: 0.0927 AC XY: 6897AN XY: 74416
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at