chr17-78171920-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004710.7(SYNGR2):c.659C>T(p.Pro220Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,613,474 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_004710.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNGR2 | NM_004710.7 | c.659C>T | p.Pro220Leu | missense_variant | Exon 4 of 4 | ENST00000225777.8 | NP_004701.1 | |
SYNGR2 | NM_001363778.1 | c.748C>T | p.Arg250Cys | missense_variant | Exon 3 of 3 | NP_001350707.1 | ||
SYNGR2 | NM_001320523.2 | c.*111C>T | 3_prime_UTR_variant | Exon 3 of 3 | NP_001307452.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000519 AC: 13AN: 250624Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135612
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461290Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 726976
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.659C>T (p.P220L) alteration is located in exon 4 (coding exon 4) of the SYNGR2 gene. This alteration results from a C to T substitution at nucleotide position 659, causing the proline (P) at amino acid position 220 to be replaced by a leucine (L). 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