13-80337351-G-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The ENST00000377104.4(SPRY2):c.355C>A(p.Arg119=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,150 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 33)
Consequence
SPRY2
ENST00000377104.4 synonymous
ENST00000377104.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.41
Genes affected
SPRY2 (HGNC:11270): (sprouty RTK signaling antagonist 2) This gene encodes a protein belonging to the sprouty family. The encoded protein contains a carboxyl-terminal cysteine-rich domain essential for the inhibitory activity on receptor tyrosine kinase signaling proteins and is required for growth factor stimulated translocation of the protein to membrane ruffles. In primary dermal endothelial cells this gene is transiently upregulated in response to fibroblast growth factor two. This protein is indirectly involved in the non-cell autonomous inhibitory effect on fibroblast growth factor two signaling. The protein interacts with Cas-Br-M (murine) ectropic retroviral transforming sequence, and can function as a bimodal regulator of epidermal growth factor receptor/mitogen-activated protein kinase signaling. This protein may play a role in alveoli branching during lung development as shown by a similar mouse protein. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP7
Synonymous conserved (PhyloP=2.41 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SPRY2 | NM_005842.4 | c.355C>A | p.Arg119= | synonymous_variant | 2/2 | ENST00000377104.4 | NP_005833.1 | |
| SPRY2 | NM_001318536.1 | c.355C>A | p.Arg119= | synonymous_variant | 2/2 | NP_001305465.1 | ||
| SPRY2 | NM_001318537.1 | c.355C>A | p.Arg119= | synonymous_variant | 2/2 | NP_001305466.1 | ||
| SPRY2 | NM_001318538.1 | c.355C>A | p.Arg119= | synonymous_variant | 2/2 | NP_001305467.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SPRY2 | ENST00000377104.4 | c.355C>A | p.Arg119= | synonymous_variant | 2/2 | 1 | NM_005842.4 | ENSP00000366308 | P1 | |
| SPRY2 | ENST00000377102.5 | c.355C>A | p.Arg119= | synonymous_variant | 2/2 | 1 | ENSP00000366306 | P1 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 33
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GnomAD4 exome Cov.: 33
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GnomAD4 genome 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74320
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at