2-65313841-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.917G>A(p.Arg306His) variant causes a missense change. The variant allele was found at a frequency of 0.0000354 in 1,612,128 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 (★).
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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPRED2 | ENST00000356388.9 | c.917G>A | p.Arg306His | missense_variant | Exon 6 of 6 | 1 | NM_181784.3 | ENSP00000348753.4 | ||
SPRED2 | ENST00000452315.5 | c.962G>A | p.Arg321His | missense_variant | Exon 6 of 6 | 1 | ENSP00000390595.1 | |||
SPRED2 | ENST00000443619.6 | c.908G>A | p.Arg303His | missense_variant | Exon 6 of 6 | 2 | ENSP00000393697.2 | |||
SPRED2 | ENST00000421087.5 | c.563G>A | p.Arg188His | missense_variant | Exon 3 of 3 | 3 | ENSP00000407627.1 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000889 AC: 22AN: 247606Hom.: 0 AF XY: 0.0000817 AC XY: 11AN XY: 134562
GnomAD4 exome AF: 0.0000247 AC: 36AN: 1459782Hom.: 0 Cov.: 34 AF XY: 0.0000234 AC XY: 17AN XY: 726316
GnomAD4 genome AF: 0.000138 AC: 21AN: 152346Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.917G>A (p.R306H) alteration is located in exon 6 (coding exon 6) of the SPRED2 gene. This alteration results from a G to A substitution at nucleotide position 917, causing the arginine (R) at amino acid position 306 to be replaced by a histidine (H). 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