NM_001129898.2:c.254-1610_254-1608delAGAinsT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001129898.2(KRBOX4):​c.254-1610_254-1608delAGAinsT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: not found (cov: 23)

Consequence

KRBOX4
NM_001129898.2 intron

Scores

Not classified

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 0.590
Variant links:
Genes affected
KRBOX4 (HGNC:26007): (KRAB box domain containing 4) This encodes a zinc finger protein with an N-terminal KRAB (Kruppel-associated) domain found in transcriptional repressors. This gene is located in a region of the X chromosome thought to be involved in nonsyndromic X-linked cognitive disability. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KRBOX4NM_001129898.2 linkc.254-1610_254-1608delAGAinsT intron_variant Intron 5 of 5 ENST00000344302.9 NP_001123370.1 Q5JUW0-1
KRBOX4NM_017776.3 linkc.239-1610_239-1608delAGAinsT intron_variant Intron 5 of 5 NP_060246.2 Q5JUW0-2
KRBOX4NM_001129899.2 linkc.254-2_254delAGAinsT p.Asp85fs frameshift_variant, splice_acceptor_variant, splice_region_variant, intron_variant Exon 6 of 7 NP_001123371.1 Q5JUW0-3
KRBOX4NM_001129900.2 linkc.239-2_239delAGAinsT p.Asp80fs frameshift_variant, splice_acceptor_variant, splice_region_variant, intron_variant Exon 6 of 7 NP_001123372.1 Q5JUW0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KRBOX4ENST00000344302.9 linkc.254-1610_254-1608delAGAinsT intron_variant Intron 5 of 5 2 NM_001129898.2 ENSP00000345797.4 Q5JUW0-1

Frequencies

GnomAD3 genomes
Cov.:
23
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
23

ClinVar

Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link

Submissions by phenotype

not provided Other:1
-
GenomeConnect, ClinGen
Significance: not provided
Review Status: no classification provided
Collection Method: phenotyping only

Variant interpreted as Uncertain significance and reported on 09-11-2016 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-46330575; API