X-150891573-G-A

Position:

• chrX-150891573-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031462.4(CD99L2):​c.67+6949C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 110,617 control chromosomes in the GnomAD database, including 3,945 homozygotes. There are 9,560 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 0.30 (3945 hom., 9560 hem., cov: 23)
• Consequence: CD99L2 NM_031462.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD99L2	NM_031462.4	c.67+6949C>T		intron_variant		ENST00000370377.8	NP_113650.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD99L2	ENST00000370377.8	c.67+6949C>T		intron_variant		1	NM_031462.4	ENSP00000359403	P1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 33137 AN: 110566 Hom.: 3945 Cov.: 23 AF XY: 0.290 AC XY: 9519 AN XY: 32866

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.300 AC: 33173 AN: 110617 Hom.: 3945 Cov.: 23 AF XY: 0.290 AC XY: 9560 AN XY: 32927

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.320

Alfa AF: 0.276 Hom.: 1730

Bravo AF: 0.305

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.73

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

Other links and lift over

dbSNP: rs7880807; hg19: chrX-150060046;