chr2-65316798-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_181784.3(SPRED2):c.524G>A(p.Arg175Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000207 in 1,613,232 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_181784.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPRED2 | NM_181784.3 | c.524G>A | p.Arg175Gln | missense_variant | 5/6 | ENST00000356388.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPRED2 | ENST00000356388.9 | c.524G>A | p.Arg175Gln | missense_variant | 5/6 | 1 | NM_181784.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000800 AC: 20AN: 249894Hom.: 0 AF XY: 0.0000667 AC XY: 9AN XY: 135020
GnomAD4 exome AF: 0.000220 AC: 321AN: 1461142Hom.: 0 Cov.: 31 AF XY: 0.000219 AC XY: 159AN XY: 726762
GnomAD4 genome ? AF: 0.0000855 AC: 13AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 21, 2023 | The c.524G>A (p.R175Q) alteration is located in exon 5 (coding exon 5) of the SPRED2 gene. This alteration results from a G to A substitution at nucleotide position 524, causing the arginine (R) at amino acid position 175 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