X-2649336-T-C

Variant names:

• chrX-2649336-T-C
• rs952706
• ENST00000435581.7:n.586-5691T>C

Variant summary

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

The ENST00000435581.7(CD99P1):​n.586-5691T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,050 control chromosomes in the GnomAD database, including 19,073 homozygotes. There are 34,801 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 0.47 (19073 hom., 34801 hem., cov: 33)
• Consequence: CD99P1 ENST00000435581.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 0 publications found

Genes affected

CD99P1 (HGNC:):

CD99P1 (HGNC:7083): (CD99 molecule pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD99P1	NR_033380.1	n.713-5691T>C		intron_variant	Intron 8 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD99P1	ENST00000435581.7	n.586-5691T>C		intron_variant	Intron 8 of 8	2
CD99P1	ENST00000688123.2	n.488-9167T>C		intron_variant	Intron 8 of 8
CD99P1	ENST00000701084.2	n.642-9167T>C		intron_variant	Intron 9 of 9

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71106 AN: 151932 Hom.: 19074 Cov.: 33

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.0696

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.468 AC: 71115 AN: 152050 Hom.: 19073 Cov.: 33 AF XY: 0.468 AC XY: 34801 AN XY: 74288

African (AFR) AF: 0.244 AC: 10131 AN: 41512

American (AMR) AF: 0.443 AC: 6754 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1678 AN: 3464

East Asian (EAS) AF: 0.0694 AC: 360 AN: 5186

South Asian (SAS) AF: 0.519 AC: 2502 AN: 4824

European-Finnish (FIN) AF: 0.581 AC: 6136 AN: 10564

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 41953 AN: 67930

Other (OTH) AF: 0.461 AC: 971 AN: 2106

Bravo AF: 0.440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.17
PhyloP100		-0.021

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs952706; hg19: chrX-2567377;