3-142838860-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_013363.4(PCOLCE2):āc.620A>Cā(p.Tyr207Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,612,908 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_013363.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251400Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135866
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460574Hom.: 0 Cov.: 29 AF XY: 0.00000550 AC XY: 4AN XY: 726682
GnomAD4 genome AF: 0.00000656 AC: 1AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.620A>C (p.Y207S) alteration is located in exon 5 (coding exon 5) of the PCOLCE2 gene. This alteration results from a A to C substitution at nucleotide position 620, causing the tyrosine (Y) at amino acid position 207 to be replaced by a serine (S). 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