chr11-65128440-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_172230.3(SYVN1):āc.1796A>Gā(p.Asp599Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000483 in 1,613,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D599N) has been classified as Uncertain significance.
Frequency
Consequence
NM_172230.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYVN1 | NM_172230.3 | c.1796A>G | p.Asp599Gly | missense_variant | 16/16 | ENST00000377190.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYVN1 | ENST00000377190.8 | c.1796A>G | p.Asp599Gly | missense_variant | 16/16 | 1 | NM_172230.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250178Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135400
GnomAD4 exome AF: 0.0000499 AC: 73AN: 1461818Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 727212
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.1796A>G (p.D599G) alteration is located in exon 16 (coding exon 15) of the SYVN1 gene. This alteration results from a A to G substitution at nucleotide position 1796, causing the aspartic acid (D) at amino acid position 599 to be replaced by a glycine (G). 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