5-142314247-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001127496.3(SPRY4):c.862G>A(p.Gly288Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,612,134 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001127496.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPRY4 | NM_001127496.3 | c.862G>A | p.Gly288Arg | missense_variant | 2/2 | ENST00000434127.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPRY4 | ENST00000434127.3 | c.862G>A | p.Gly288Arg | missense_variant | 2/2 | 1 | NM_001127496.3 | P1 | |
SPRY4 | ENST00000344120.4 | c.931G>A | p.Gly311Arg | missense_variant | 3/3 | 1 | |||
SPRY4 | ENST00000643792.1 | n.1544G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 248196Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134576
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1459914Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 726204
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2023 | The c.931G>A (p.G311R) alteration is located in exon 3 (coding exon 2) of the SPRY4 gene. This alteration results from a G to A substitution at nucleotide position 931, causing the glycine (G) at amino acid position 311 to be replaced by an arginine (R). 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