Variant chr5-94396289-TGTTAAAA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate

The NM_001145678.3(KIAA0825):c.3101_3107delTTTTAAC(p.Leu1034fs) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 32)

Consequence

KIAA0825
NM_001145678.3 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.48

Variant links:

Genes affected

KIAA0825 (HGNC:28532): (KIAA0825)

KIAA0825 links:

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 ACMG points.

PVS1

Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 5-94396289-TGTTAAAA-T is Pathogenic according to our data. Variant chr5-94396289-TGTTAAAA-T is described in ClinVar as [Pathogenic]. Clinvar id is 3629776.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA0825	NM_001145678.3 link	c.3101_3107delTTTTAAC	p.Leu1034fs	frameshift_variant	17/21	ENST00000682413.1	NP_001139150.1	A0A804HHT9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
KIAA0825	ENST00000682413.1 link	c.3101_3107delTTTTAAC	p.Leu1034fs	frameshift_variant	17/21		NM_001145678.3	ENSP00000506760.1	A0A804HHT9
KIAA0825	ENST00000703867.1 link	c.3116_3122delTTTTAAC	p.Leu1039fs	frameshift_variant	17/21			ENSP00000515512.1	A0A994J718
KIAA0825	ENST00000513200.7 link	c.3101_3107delTTTTAAC	p.Leu1034fs	frameshift_variant	16/20	5		ENSP00000424618.2	Q8IV33-1

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

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

LitVar

Below is the list of publications found by LitVar. It may be empty.