NM_014850.4:c.2817G>A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_014850.4(SRGAP3):c.2817G>A(p.Ser939Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00029 in 1,594,028 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_014850.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRGAP3 | ENST00000383836.8 | c.2817G>A | p.Ser939Ser | synonymous_variant | Exon 21 of 22 | 1 | NM_014850.4 | ENSP00000373347.3 | ||
SRGAP3 | ENST00000360413.7 | c.2745G>A | p.Ser915Ser | synonymous_variant | Exon 21 of 22 | 1 | ENSP00000353587.3 |
Frequencies
GnomAD3 genomes AF: 0.00155 AC: 236AN: 152256Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000296 AC: 63AN: 213034Hom.: 0 AF XY: 0.000174 AC XY: 20AN XY: 114858
GnomAD4 exome AF: 0.000157 AC: 227AN: 1441654Hom.: 3 Cov.: 32 AF XY: 0.000164 AC XY: 117AN XY: 715150
GnomAD4 genome AF: 0.00155 AC: 236AN: 152374Hom.: 0 Cov.: 33 AF XY: 0.00162 AC XY: 121AN XY: 74516
ClinVar
Submissions by phenotype
SRGAP3-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at