chr10-126504556-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001350921.2(C10orf90):c.935G>A(p.Gly312Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00362 in 1,614,214 control chromosomes in the GnomAD database, including 20 homozygotes. 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 Likely benign (★★).
Frequency
Consequence
NM_001350921.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C10orf90 | NM_001350921.2 | c.935G>A | p.Gly312Glu | missense_variant | 4/10 | ENST00000488181.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C10orf90 | ENST00000488181.3 | c.935G>A | p.Gly312Glu | missense_variant | 4/10 | 2 | NM_001350921.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00246 AC: 374AN: 152202Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00275 AC: 691AN: 251470Hom.: 3 AF XY: 0.00286 AC XY: 389AN XY: 135916
GnomAD4 exome AF: 0.00374 AC: 5467AN: 1461894Hom.: 19 Cov.: 34 AF XY: 0.00373 AC XY: 2709AN XY: 727248
GnomAD4 genome AF: 0.00246 AC: 374AN: 152320Hom.: 1 Cov.: 33 AF XY: 0.00250 AC XY: 186AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at