Variant rs11911 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005842.4(SPRY2):c.*42T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 1,571,972 control chromosomes in the GnomAD database, including 118,873 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 0.31 ( 8881 hom., cov: 33)

Exomes 𝑓: 0.39 ( 109992 hom. )

Consequence

SPRY2
NM_005842.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.162

Variant links:

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]

SPRY2 links:

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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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
SPRY2	NM_005842.4 linkuse as main transcript	c.*42T>G	3_prime_UTR_variant	2/2	ENST00000377104.4	NP_005833.1
SPRY2	NM_001318536.1 linkuse as main transcript	c.*42T>G	3_prime_UTR_variant	2/2		NP_001305465.1
SPRY2	NM_001318537.1 linkuse as main transcript	c.*42T>G	3_prime_UTR_variant	2/2		NP_001305466.1
SPRY2	NM_001318538.1 linkuse as main transcript	c.*42T>G	3_prime_UTR_variant	2/2		NP_001305467.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPRY2	ENST00000377104.4 linkuse as main transcript	c.*42T>G		3_prime_UTR_variant	2/2	1	NM_005842.4	ENSP00000366308	P1
SPRY2	ENST00000377102.5 linkuse as main transcript	c.*42T>G		3_prime_UTR_variant	2/2	1		ENSP00000366306	P1

Frequencies

GnomAD3 genomes

AF:

0.310

AC:

47051

AN:

151974

Hom.:

8870

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0755

Gnomad AMI

AF:

0.426

Gnomad AMR

AF:

0.434

Gnomad ASJ

AF:

0.355

Gnomad EAS

AF:

0.455

Gnomad SAS

AF:

0.356

Gnomad FIN

AF:

0.404

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.390

Gnomad OTH

AF:

0.344

GnomAD3 exomes

AF:

0.394

AC:

82860

AN:

210360

Hom.:

17320

AF XY:

0.392

AC XY:

44524

AN XY:

113632

show subpopulations

Gnomad AFR exome

AF:

0.0703

Gnomad AMR exome

AF:

0.525

Gnomad ASJ exome

AF:

0.340

Gnomad EAS exome

AF:

0.473

Gnomad SAS exome

AF:

0.374

Gnomad FIN exome

AF:

0.403

Gnomad NFE exome

AF:

0.390

Gnomad OTH exome

AF:

0.397

GnomAD4 exome

AF:

0.389

AC:

551943

AN:

1419882

Hom.:

109992

Cov.:

AF XY:

0.388

AC XY:

273979

AN XY:

705246

show subpopulations

Gnomad4 AFR exome

AF:

0.0615

Gnomad4 AMR exome

AF:

0.516

Gnomad4 ASJ exome

AF:

0.346

Gnomad4 EAS exome

AF:

0.427

Gnomad4 SAS exome

AF:

0.375

Gnomad4 FIN exome

AF:

0.395

Gnomad4 NFE exome

AF:

0.395

Gnomad4 OTH exome

AF:

0.381

GnomAD4 genome

AF:

0.310

AC:

47072

AN:

152090

Hom.:

8881

Cov.:

AF XY:

0.314

AC XY:

23320

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.0753

Gnomad4 AMR

AF:

0.434

Gnomad4 ASJ

AF:

0.355

Gnomad4 EAS

AF:

0.455

Gnomad4 SAS

AF:

0.359

Gnomad4 FIN

AF:

0.404

Gnomad4 NFE

AF:

0.390

Gnomad4 OTH

AF:

0.341

Alfa

AF:

0.378

Hom.:

10906

Bravo

AF:

0.304

Asia WGS

AF:

0.335

AC:

1166

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

9.1

DANN

Benign

0.64

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over