rs934734
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_181784.3(SPRED2):c.27-23556C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,076 control chromosomes in the GnomAD database, including 23,004 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.55 ( 23004 hom., cov: 33)
Consequence
SPRED2
NM_181784.3 intron
NM_181784.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.759
Genes affected
SPRED2 (HGNC:17722): (sprouty related EVH1 domain containing 2) SPRED2 is a member of the Sprouty (see SPRY1; MIM 602465)/SPRED family of proteins that regulate growth factor-induced activation of the MAP kinase cascade (see MAPK1; MIM 176948) (Nonami et al., 2004 [PubMed 15465815]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPRED2 | NM_181784.3 | c.27-23556C>T | intron_variant | ENST00000356388.9 | |||
SPRED2 | XM_005264200.6 | c.27-23556C>T | intron_variant | ||||
SPRED2 | XM_005264202.6 | c.27-23556C>T | intron_variant | ||||
SPRED2 | XM_047443709.1 | c.-35+12174C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPRED2 | ENST00000356388.9 | c.27-23556C>T | intron_variant | 1 | NM_181784.3 | P4 | |||
SPRED2 | ENST00000452315.5 | c.71+9161C>T | intron_variant | 1 | |||||
SPRED2 | ENST00000440972.1 | c.27-23556C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.547 AC: 83153AN: 151958Hom.: 22963 Cov.: 33
GnomAD3 genomes
?
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151958
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.547 AC: 83250AN: 152076Hom.: 23004 Cov.: 33 AF XY: 0.552 AC XY: 41050AN XY: 74336
GnomAD4 genome
?
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AC:
83250
AN:
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33
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41050
AN XY:
74336
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2233
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at