Genetic Variant TCP11X2:c.1112+248G>C (chrX-102462597-C-G) – ACMG Classification: Likely_benign (-4 pts)

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.276

Publications

1 publications found

Variant links:

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]

TCP11X2 links:

ENSG00000284800 (HGNC:):

ENSG00000284800 links:

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ACMG classification

Classification was made for transcript

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

Gene	Transcript	Tags	HGVSc	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

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Cov.:

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

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Cov.:

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African (AFR)

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American (AMR)

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Ashkenazi Jewish (ASJ)

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East Asian (EAS)

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South Asian (SAS)

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European-Finnish (FIN)

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Middle Eastern (MID)

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European-Non Finnish (NFE)

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Other (OTH)

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Alfa

AF:

0.196

Hom.:

931

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over