12-33376853-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_198992.4(SYT10):āc.1549C>Gā(p.Pro517Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000335 in 1,614,092 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_198992.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYT10 | ENST00000228567.7 | c.1549C>G | p.Pro517Ala | missense_variant | Exon 7 of 7 | 1 | NM_198992.4 | ENSP00000228567.3 | ||
SYT10 | ENST00000539102.1 | n.*1144C>G | non_coding_transcript_exon_variant | Exon 9 of 9 | 1 | ENSP00000444577.1 | ||||
SYT10 | ENST00000539102.1 | n.*1144C>G | 3_prime_UTR_variant | Exon 9 of 9 | 1 | ENSP00000444577.1 |
Frequencies
GnomAD3 genomes AF: 0.000329 AC: 50AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000438 AC: 110AN: 251240Hom.: 1 AF XY: 0.000420 AC XY: 57AN XY: 135778
GnomAD4 exome AF: 0.000335 AC: 490AN: 1461818Hom.: 2 Cov.: 30 AF XY: 0.000322 AC XY: 234AN XY: 727212
GnomAD4 genome AF: 0.000328 AC: 50AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.000322 AC XY: 24AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1549C>G (p.P517A) alteration is located in exon 7 (coding exon 7) of the SYT10 gene. This alteration results from a C to G substitution at nucleotide position 1549, causing the proline (P) at amino acid position 517 to be replaced by an alanine (A). 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