rs11796490

Variant names:

• chrX-150889686-A-G
• rs11796490
• NM_031462.4:c.67+8836T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031462.4(CD99L2):​c.67+8836T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 111,127 control chromosomes in the GnomAD database, including 3,462 homozygotes. There are 9,392 hemizygotes in GnomAD. 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 0.29 (3462 hom., 9392 hem., cov: 23)
• Consequence: CD99L2 NM_031462.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.757
• Publications: 2 publications found

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]

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD99L2	NM_031462.4	MANE Select	c.67+8836T>C		intron	N/A	NP_113650.2
	CD99L2	NM_001242614.2		c.67+8836T>C		intron	N/A	NP_001229543.1
	CD99L2	NM_134446.4		c.67+8836T>C		intron	N/A	NP_604395.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD99L2	ENST00000370377.8	TSL:1 MANE Select	c.67+8836T>C		intron	N/A	ENSP00000359403.3
	CD99L2	ENST00000466436.5	TSL:1	c.67+8836T>C		intron	N/A	ENSP00000417697.1
	CD99L2	ENST00000355149.8	TSL:1	c.67+8836T>C		intron	N/A	ENSP00000347275.3

Frequencies

GnomAD3 genomes AF: 0.287 AC: 31826 AN: 111074 Hom.: 3464 Cov.: 23

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.371

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.287 AC: 31853 AN: 111127 Hom.: 3462 Cov.: 23 AF XY: 0.281 AC XY: 9392 AN XY: 33379

African (AFR) AF: 0.386 AC: 11801 AN: 30571

American (AMR) AF: 0.238 AC: 2515 AN: 10553

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1060 AN: 2632

East Asian (EAS) AF: 0.119 AC: 418 AN: 3512

South Asian (SAS) AF: 0.354 AC: 940 AN: 2654

European-Finnish (FIN) AF: 0.280 AC: 1635 AN: 5829

Middle Eastern (MID) AF: 0.365 AC: 77 AN: 211

European-Non Finnish (NFE) AF: 0.243 AC: 12869 AN: 52970

Other (OTH) AF: 0.309 AC: 468 AN: 1513

Alfa AF: 0.267 Hom.: 26641

Bravo AF: 0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.42
PhyloP100		0.76
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11796490; hg19: chrX-150058159;