Variant X-2726261-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_002414.5(CD99):c.363C>T(p.Ala121Ala) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 1,601,818 control chromosomes in the GnomAD database, including 15,481 homozygotes. There are 95,822 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in Lovd as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.13 ( 1258 hom., 8308 hem., cov: 32)

Exomes 𝑓: 0.14 ( 14223 hom. 87514 hem. )

Consequence

CD99
NM_002414.5 splice_region, synonymous

Scores

Splicing: ADA: 0.000006554

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.22

Variant links:

Genes affected

CD99 (HGNC:7082): (CD99 molecule (Xg blood group)) The protein encoded by this gene is a cell surface glycoprotein involved in leukocyte migration, T-cell adhesion, ganglioside GM1 and transmembrane protein transport, and T-cell death by a caspase-independent pathway. In addition, the encoded protein may have the ability to rearrange the actin cytoskeleton and may also act as an oncosuppressor in osteosarcoma. This gene is found in the pseudoautosomal region of chromosomes X and Y and escapes X-chromosome inactivation. There is a related pseudogene located immediately adjacent to this locus. [provided by RefSeq, Mar 2016]

CD99 links:

CD99 (HGNC:):

CD99 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.07).

BP6

Variant X-2726261-C-T is Benign according to our data. Variant chrX-2726261-C-T is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-2.22 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD99	NM_002414.5 linkuse as main transcript	c.363C>T	p.Ala121Ala	splice_region_variant, synonymous_variant	8/10	ENST00000381192.10	NP_002405.1	P14209-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD99	ENST00000381192.10 linkuse as main transcript	c.363C>T	p.Ala121Ala	splice_region_variant, synonymous_variant	8/10	1	NM_002414.5	ENSP00000370588.3		P14209-1
CD99	ENST00000381184.6 linkuse as main transcript	c.363C>T	p.Ala121Ala	splice_region_variant, synonymous_variant	8/10	5		ENSP00000370579.1		A8MQT7

Frequencies

GnomAD3 genomes

AF:

0.127

AC:

19220

AN:

151928

Hom.:

1261

Cov.:

AF XY:

0.112

AC XY:

8289

AN XY:

74192

show subpopulations

Gnomad AFR

AF:

0.0903

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.166

Gnomad ASJ

AF:

0.149

Gnomad EAS

AF:

0.0797

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.154

Gnomad NFE

AF:

0.143

Gnomad OTH

AF:

0.147

GnomAD3 exomes

AF:

0.143

AC:

35827

AN:

250760

Hom.:

2807

AF XY:

0.129

AC XY:

17541

AN XY:

135510

show subpopulations

Gnomad AFR exome

AF:

0.0886

Gnomad AMR exome

AF:

0.231

Gnomad ASJ exome

AF:

0.156

Gnomad EAS exome

AF:

0.0777

Gnomad SAS exome

AF:

0.143

Gnomad FIN exome

AF:

0.123

Gnomad NFE exome

AF:

0.137

Gnomad OTH exome

AF:

0.149

GnomAD4 exome

AF:

0.138

AC:

199616

AN:

1449770

Hom.:

14223

Cov.:

AF XY:

0.121

AC XY:

87514

AN XY:

721614

show subpopulations

Gnomad4 AFR exome

AF:

0.0899

Gnomad4 AMR exome

AF:

0.225

Gnomad4 ASJ exome

AF:

0.153

Gnomad4 EAS exome

AF:

0.0576

Gnomad4 SAS exome

AF:

0.146

Gnomad4 FIN exome

AF:

0.128

Gnomad4 NFE exome

AF:

0.138

Gnomad4 OTH exome

AF:

0.139

GnomAD4 genome

AF:

0.126

AC:

19224

AN:

152048

Hom.:

1258

Cov.:

AF XY:

0.112

AC XY:

8308

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.0901

Gnomad4 AMR

AF:

0.167

Gnomad4 ASJ

AF:

0.149

Gnomad4 EAS

AF:

0.0799

Gnomad4 SAS

AF:

0.141

Gnomad4 FIN

AF:

0.113

Gnomad4 NFE

AF:

0.143

Gnomad4 OTH

AF:

0.145

Bravo

AF:

0.131

EpiCase

AF:

0.139

EpiControl

AF:

0.139

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.013

DANN

Benign

0.53

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.7

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0000066

dbscSNV1_RF

Benign

0.0

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over