Variant chr8-142764641-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_177458.3(SLURP2):c.258C>T(p.Ile86Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000168 in 1,608,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00082 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00010 ( 0 hom. )

Consequence

SLURP2
NM_177458.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.37

Variant links:

Genes affected

SLURP2 (HGNC:25549): (secreted LY6/PLAUR domain containing 2) This gene encodes a novel, secreted member of the Ly6/uPAR (LU) superfamily of proteins containing the unique three-finger LU domain. This gene is mainly expressed in epithelial cells, including skin and keratinocytes, and is up-regulated in psoriatic skin lesions, suggesting its involvement in the pathophysiology of psoriasis. Alternatively spliced transcript variants have been found for this gene. Read-through transcription from the neighboring upstream gene (LYNX1) generates naturally-occurring transcripts (LYNX1-SLURP2) that encode a fusion protein comprised of sequence sharing identity with each individual gene product. [provided by RefSeq, Sep 2017]

SLURP2 links:

LYNX1-SLURP2 (HGNC:52291): (LYNX1-SLURP2 readthrough) This locus represents naturally occurring read-through transcription between the neighboring LYNX1 and SLURP2 genes. The readthrough transcript encodes a fusion protein comprised of sequence sharing identity with each individual gene product. The significance of this read-through transcription and the function of the resulting protein product have not yet been determined. [provided by RefSeq, Sep 2017]

LYNX1-SLURP2 links:

ENSG00000253196 (HGNC:):

ENSG00000253196 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 8-142764641-G-A is Benign according to our data. Variant chr8-142764641-G-A is described in ClinVar as [Benign]. Clinvar id is 748291.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.37 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLURP2	NM_177458.3 linkuse as main transcript	c.258C>T	p.Ile86Ile	synonymous_variant	3/3	ENST00000317543.12	NP_803253.1	P0DP57
LYNX1-SLURP2	NM_023946.5 linkuse as main transcript	c.360C>T	p.Ile120Ile	synonymous_variant	5/5		NP_076435.1	P0DP58-2
SLURP2	NM_001356372.2 linkuse as main transcript	c.158-54C>T		intron_variant			NP_001343301.1
LOC124902033	XR_007061134.1 linkuse as main transcript	n.431+1146G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLURP2	ENST00000317543.12 linkuse as main transcript	c.258C>T	p.Ile86Ile	synonymous_variant	3/3	1	NM_177458.3	ENSP00000319846.7		P0DP57
LYNX1-SLURP2	ENST00000615007.4 linkuse as main transcript	c.360C>T	p.Ile120Ile	synonymous_variant	5/5	1		ENSP00000479586.1

Frequencies

GnomAD3 genomes

AF:

0.000821

AC:

125

AN:

152166

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00287

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000327

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.000233

AC:

AN:

244474

Hom.:

AF XY:

0.000158

AC XY:

AN XY:

132880

show subpopulations

Gnomad AFR exome

AF:

0.00330

Gnomad AMR exome

AF:

0.0000616

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000556

Gnomad SAS exome

AF:

0.0000331

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000995

AC:

145

AN:

1456600

Hom.:

Cov.:

AF XY:

0.0000731

AC XY:

AN XY:

724758

show subpopulations

Gnomad4 AFR exome

AF:

0.00356

Gnomad4 AMR exome

AF:

0.0000932

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000349

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000360

Gnomad4 OTH exome

AF:

0.000216

GnomAD4 genome

AF:

0.000821

AC:

125

AN:

152284

Hom.:

Cov.:

AF XY:

0.000954

AC XY:

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00286

Gnomad4 AMR

AF:

0.000327

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.000461

Hom.:

Bravo

AF:

0.00101

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.70

DANN

Benign

0.63

Splicing

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over