rs652759

Variant names:

• chrX-102462597-C-G
• rs652759
• NM_001405027.1:c.1112+248G>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001405027.1(TCP11X2):​c.1112+248G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 0)
  • Failed GnomAD Quality Control
• Consequence: TCP11X2 NM_001405027.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 1 publications found

Genes affected

TCP11X2 (HGNC:48335): (t-complex 11 family, X-linked 2) Predicted to be involved in protein kinase A signaling and regulation of sperm capacitation. Predicted to be active in acrosomal vesicle and sperm flagellum. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000284800 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001405027.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCP11X2	NM_001405027.1	MANE Select	c.1112+248G>C		intron	N/A	NP_001391956.1	Q5H9J9
	TCP11X2	NM_001277423.2		c.827+248G>C		intron	N/A	NP_001264352.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCP11X2	ENST00000642911.3	MANE Select	c.1112+248G>C		intron	N/A	ENSP00000496057.1	Q5H9J9
	ENSG00000284800	ENST00000618302.2	TSL:2	n.221+248G>C		intron	N/A	ENSP00000484645.2	A0A2U3TZR1
	ENSG00000284800	ENST00000429905.5	TSL:2	n.*1132+248G>C		intron	N/A	ENSP00000404462.1	F2Z2N1

Frequencies

GnomAD3 genomes AC: 0 AN: 0 Hom.: 0 Cov.: 0

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

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

Alfa AF: 0.196 Hom.: 931

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.45
PhyloP100		-0.28

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: rs652759; hg19: chrX-101717518;