rs1555391042

Positions:

• chr15-38322323-AG-GA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1 PM2 BP6_Moderate

The NM_152594.3(SPRED1):​c.290_291delinsGA​(p.Lys97Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Benignin ClinVar. Synonymous variant affecting the same amino acid position (i.e. K97K) has been classified as Benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: SPRED1 NM_152594.3 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 4.31

Genes affected

SPRED1 (HGNC:20249): (sprouty related EVH1 domain containing 1) The protein encoded by this gene is a member of the Sprouty family of proteins and is phosphorylated by tyrosine kinase in response to several growth factors. The encoded protein can act as a homodimer or as a heterodimer with SPRED2 to regulate activation of the MAP kinase cascade. Defects in this gene are a cause of neurofibromatosis type 1-like syndrome (NFLS). [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM1: In a strand (size 8) in uniprot entity SPRE1_HUMAN there are 5 pathogenic changes around while only 2 benign (71%) in NM_152594.3
• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 15-38322323-AG-GA is Benign according to our data. Variant chr15-38322323-AG-GA is described in ClinVar as [Likely_benign]. Clinvar id is 536697.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPRED1	NM_152594.3	c.290_291delinsGA	p.Lys97Arg	missense_variant	3/7	ENST00000299084.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPRED1	ENST00000299084.9	c.290_291delinsGA	p.Lys97Arg	missense_variant	3/7	1	NM_152594.3	P1
SPRED1	ENST00000561317.1	c.227_228delinsGA	p.Lys76Arg	missense_variant	4/6	4
SPRED1	ENST00000561205.1	n.628_629delinsGA		non_coding_transcript_exon_variant	3/5	5

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Legius syndrome Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Oct 08, 2023

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555391042; hg19: chr15-38614524;