10-49679744-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001042427.3(C10orf53):c.47C>T(p.Ala16Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000252 in 1,547,228 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001042427.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C10orf53 | ENST00000374111.8 | c.47C>T | p.Ala16Val | missense_variant | Exon 1 of 3 | 2 | NM_001042427.3 | ENSP00000363225.3 | ||
C10orf53 | ENST00000374112.7 | c.47C>T | p.Ala16Val | missense_variant | Exon 1 of 3 | 2 | ENSP00000363226.3 | |||
C10orf53 | ENST00000374113.3 | c.47C>T | p.Ala16Val | missense_variant | Exon 1 of 2 | 2 | ENSP00000363227.3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152256Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000133 AC: 20AN: 150482Hom.: 0 AF XY: 0.000163 AC XY: 13AN XY: 79914
GnomAD4 exome AF: 0.0000251 AC: 35AN: 1394854Hom.: 0 Cov.: 31 AF XY: 0.0000305 AC XY: 21AN XY: 688056
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152374Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74514
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.47C>T (p.A16V) alteration is located in exon 1 (coding exon 1) of the C10orf53 gene. This alteration results from a C to T substitution at nucleotide position 47, causing the alanine (A) at amino acid position 16 to be replaced by a valine (V). 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