chr3-8990735-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014850.4(SRGAP3):c.2663G>A(p.Arg888Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000267 in 1,609,890 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R888W) has been classified as Uncertain significance.
Frequency
Consequence
NM_014850.4 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 |
---|---|---|---|---|---|---|---|
SRGAP3 | NM_014850.4 | c.2663G>A | p.Arg888Gln | missense_variant | 21/22 | ENST00000383836.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRGAP3 | ENST00000383836.8 | c.2663G>A | p.Arg888Gln | missense_variant | 21/22 | 1 | NM_014850.4 | P1 | |
SRGAP3 | ENST00000360413.7 | c.2591G>A | p.Arg864Gln | missense_variant | 21/22 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000384 AC: 9AN: 234442Hom.: 0 AF XY: 0.0000389 AC XY: 5AN XY: 128614
GnomAD4 exome AF: 0.0000268 AC: 39AN: 1457708Hom.: 0 Cov.: 32 AF XY: 0.0000207 AC XY: 15AN XY: 724896
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.2663G>A (p.R888Q) alteration is located in exon 21 (coding exon 21) of the SRGAP3 gene. This alteration results from a G to A substitution at nucleotide position 2663, causing the arginine (R) at amino acid position 888 to be replaced by a glutamine (Q). 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