20-59864364-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_014258.4(SYCP2):c.4540C>T(p.Arg1514Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000106 in 1,599,494 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014258.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYCP2 | ENST00000357552.8 | c.4540C>T | p.Arg1514Cys | missense_variant | Exon 45 of 45 | 1 | NM_014258.4 | ENSP00000350162.2 | ||
SYCP2 | ENST00000371001.6 | c.4540C>T | p.Arg1514Cys | missense_variant | Exon 44 of 44 | 1 | ENSP00000360040.2 | |||
SYCP2 | ENST00000412613.1 | c.598C>T | p.Arg200Cys | missense_variant | Exon 8 of 8 | 3 | ENSP00000404358.1 |
Frequencies
GnomAD3 genomes AF: 0.0000266 AC: 4AN: 150156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000124 AC: 3AN: 241828Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 131000
GnomAD4 exome AF: 0.00000897 AC: 13AN: 1449338Hom.: 0 Cov.: 29 AF XY: 0.0000153 AC XY: 11AN XY: 720774
GnomAD4 genome AF: 0.0000266 AC: 4AN: 150156Hom.: 0 Cov.: 32 AF XY: 0.0000137 AC XY: 1AN XY: 73162
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4540C>T (p.R1514C) alteration is located in exon 44 (coding exon 43) of the SYCP2 gene. This alteration results from a C to T substitution at nucleotide position 4540, causing the arginine (R) at amino acid position 1514 to be replaced by a cysteine (C). 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