NM_198992.4:c.771T>A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198992.4(SYT10):c.771T>A(p.Asp257Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,636 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198992.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYT10 | ENST00000228567.7 | c.771T>A | p.Asp257Glu | missense_variant | Exon 3 of 7 | 1 | NM_198992.4 | ENSP00000228567.3 | ||
SYT10 | ENST00000539102.1 | n.*366T>A | non_coding_transcript_exon_variant | Exon 5 of 9 | 1 | ENSP00000444577.1 | ||||
SYT10 | ENST00000539102.1 | n.*366T>A | 3_prime_UTR_variant | Exon 5 of 9 | 1 | ENSP00000444577.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461462Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727060
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.771T>A (p.D257E) alteration is located in exon 3 (coding exon 3) of the SYT10 gene. This alteration results from a T to A substitution at nucleotide position 771, causing the aspartic acid (D) at amino acid position 257 to be replaced by a glutamic acid (E). 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