NM_005842.4:c.410G>C

Variant names:

• chr13-80337296-C-G
• rs747621224
• NM_005842.4:c.410G>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_005842.4(SPRY2):​c.410G>C​(p.Gly137Ala) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: SPRY2 NM_005842.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.38

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.21271214).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPRY2	NM_005842.4	c.410G>C	p.Gly137Ala	missense_variant	Exon 2 of 2	ENST00000377104.4	NP_005833.1
SPRY2	NM_001318536.1	c.410G>C	p.Gly137Ala	missense_variant	Exon 2 of 2		NP_001305465.1
SPRY2	NM_001318537.1	c.410G>C	p.Gly137Ala	missense_variant	Exon 2 of 2		NP_001305466.1
SPRY2	NM_001318538.1	c.410G>C	p.Gly137Ala	missense_variant	Exon 2 of 2		NP_001305467.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPRY2	ENST00000377104.4	c.410G>C	p.Gly137Ala	missense_variant	Exon 2 of 2	1	NM_005842.4	ENSP00000366308.3
SPRY2	ENST00000377102.5	c.410G>C	p.Gly137Ala	missense_variant	Exon 2 of 2	1		ENSP00000366306.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

IgA nephropathy, susceptibility to, 3 Uncertain:1

Oct 25, 2019

Baylor Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.52
CADD	Benign	20
DANN	Benign	0.91
DEOGEN2	Benign	0.049	T;T
Eigen	Benign	-0.26
Eigen_PC	Benign	-0.14
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.85	.;T
M_CAP	Benign	0.0085	T
MetaRNN	Benign	0.21	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.6	L;L
PrimateAI	Uncertain	0.66	T
PROVEAN	Benign	-0.83	N;N
REVEL	Benign	0.056
Sift	Benign	0.23	T;T
Sift4G	Benign	0.66	T;T
Polyphen		0.020	B;B
Vest4		0.35
MutPred		0.15		Gain of helix (P = 0.0425);Gain of helix (P = 0.0425);
MVP		0.55
MPC		0.51
ClinPred		0.67	D
GERP RS		5.0
Varity_R		0.20
gMVP		0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs747621224; hg19: chr13-80911431;