rs142711233
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_181784.3(SPRED2):c.791A>G(p.Tyr264Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,612,630 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPRED2 | ENST00000356388.9 | c.791A>G | p.Tyr264Cys | missense_variant | Exon 6 of 6 | 1 | NM_181784.3 | ENSP00000348753.4 | ||
SPRED2 | ENST00000452315.5 | c.836A>G | p.Tyr279Cys | missense_variant | Exon 6 of 6 | 1 | ENSP00000390595.1 | |||
SPRED2 | ENST00000443619.6 | c.782A>G | p.Tyr261Cys | missense_variant | Exon 6 of 6 | 2 | ENSP00000393697.2 | |||
SPRED2 | ENST00000421087.5 | c.437A>G | p.Tyr146Cys | missense_variant | Exon 3 of 3 | 3 | ENSP00000407627.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248502Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134872
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1460432Hom.: 0 Cov.: 34 AF XY: 0.00000826 AC XY: 6AN XY: 726624
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.791A>G (p.Y264C) alteration is located in exon 6 (coding exon 6) of the SPRED2 gene. This alteration results from a A to G substitution at nucleotide position 791, causing the tyrosine (Y) at amino acid position 264 to be replaced by a cysteine (C). 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