Genetic Variant CD99L2:p.Leu16Phe (chrX-150898541-C-A) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_031462.4(CD99L2):c.48G>T(p.Leu16Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 23)

Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

CD99L2
NM_031462.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.50

Publications

0 publications found

Variant links:

Genes affected

CD99L2 (HGNC:18237): (CD99 molecule like 2) This gene encodes a cell-surface protein that is similar to CD99. A similar protein in mouse functions as an adhesion molecule during leukocyte extravasation. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

CD99L2 links:

LINC02927 (HGNC:55778): (long intergenic non-protein coding RNA 2927)

LINC02927 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.37236196).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031462.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CD99L2	NM_031462.4	MANE Select	c.48G>T	p.Leu16Phe	missense	Exon 1 of 11	NP_113650.2	A0A024RC16
CD99L2	NM_001242614.2		c.48G>T	p.Leu16Phe	missense	Exon 1 of 12	NP_001229543.1	Q8TCZ2-5
CD99L2	NM_134446.4		c.48G>T	p.Leu16Phe	missense	Exon 1 of 9	NP_604395.1	Q8TCZ2-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CD99L2	ENST00000370377.8	TSL:1 MANE Select	c.48G>T	p.Leu16Phe	missense	Exon 1 of 11	ENSP00000359403.3	Q8TCZ2-1
CD99L2	ENST00000466436.5	TSL:1	c.48G>T	p.Leu16Phe	missense	Exon 1 of 9	ENSP00000417697.1	Q8TCZ2-2
CD99L2	ENST00000355149.8	TSL:1	c.48G>T	p.Leu16Phe	missense	Exon 1 of 8	ENSP00000347275.3	Q8TCZ2-3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1000520

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

320262

African (AFR)

AF:

0.00

AC:

AN:

20519

American (AMR)

AF:

0.00

AC:

AN:

19630

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16964

East Asian (EAS)

AF:

0.00

AC:

AN:

21989

South Asian (SAS)

AF:

0.00

AC:

AN:

45275

European-Finnish (FIN)

AF:

0.00

AC:

AN:

35319

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2728

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

796359

Other (OTH)

AF:

0.00

AC:

AN:

41737

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.095

BayesDel_addAF

Uncertain

0.028

BayesDel_noAF

Benign

-0.20

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.073

FATHMM_MKL

Uncertain

0.80

LIST_S2

Benign

0.83

M_CAP

Pathogenic

0.66

MetaRNN

Benign

0.37

MetaSVM

Benign

-0.50

MutationAssessor

Benign

1.9

PhyloP100

1.5

PrimateAI

Uncertain

0.60

PROVEAN

Benign

-1.7

REVEL

Benign

0.12

Sift

Uncertain

0.014

Sift4G

Benign

0.17

Polyphen

1.0

Vest4

0.30

MutPred

0.29

Loss of helix (P = 0.0104)

MVP

0.84

MPC

0.080

ClinPred

0.73

GERP RS

4.0

PromoterAI

0.0010

Neutral

(source)

Varity_R

0.31

gMVP

0.21

Mutation Taster

=80/20

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over