Variant rs2308043 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000666654.1(KAZN-AS1):n.1150-1081_1150-1080insGTCTGTGA variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.39 ( 13163 hom., cov: 0)

Consequence

KAZN-AS1
ENST00000666654.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27

Variant links:

Genes affected

KAZN-AS1 (HGNC:53610): (KAZN antisense RNA 1)

KAZN-AS1 links:

KAZN (HGNC:29173): (kazrin, periplakin interacting protein) This gene encodes a protein that plays a role in desmosome assembly, cell adhesion, cytoskeletal organization, and epidermal differentiation. This protein co-localizes with desmoplakin and the cytolinker protein periplakin. In general, this protein localizes to the nucleus, desmosomes, cell membrane, and cortical actin-based structures. Some isoforms of this protein also associate with microtubules. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional splice variants have been described but their biological validity has not been verified. [provided by RefSeq, Aug 2011]

KAZN links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
KAZN	XM_005245795.6 linkuse as main transcript	c.279+159508_279+159509insACAGACTC	intron_variant
KAZN	XM_011541074.4 linkuse as main transcript	c.279+159508_279+159509insACAGACTC	intron_variant
KAZN	XM_011541080.4 linkuse as main transcript	c.279+159508_279+159509insACAGACTC	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KAZN-AS1	ENST00000666654.1 linkuse as main transcript	n.1150-1081_1150-1080insGTCTGTGA		intron_variant, non_coding_transcript_variant
KAZN	ENST00000636203.1 linkuse as main transcript	c.249+159508_249+159509insACAGACTC		intron_variant		5		A2

Frequencies

GnomAD3 genomes

AF:

0.395

AC:

59939

AN:

151880

Hom.:

13129

Cov.:

show subpopulations

Gnomad AFR

AF:

0.590

Gnomad AMI

AF:

0.326

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.384

Gnomad SAS

AF:

0.412

Gnomad FIN

AF:

0.314

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.330

Gnomad OTH

AF:

0.341

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

GnomAD4 genome

AF:

0.395

AC:

60009

AN:

151996

Hom.:

13163

Cov.:

AF XY:

0.392

AC XY:

29116

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.591

Gnomad4 AMR

AF:

0.254

Gnomad4 ASJ

AF:

0.256

Gnomad4 EAS

AF:

0.383

Gnomad4 SAS

AF:

0.412

Gnomad4 FIN

AF:

0.314

Gnomad4 NFE

AF:

0.330

Gnomad4 OTH

AF:

0.341

Alfa

AF:

0.170

Hom.:

283

Bravo

AF:

0.392

Asia WGS

AF:

0.370

AC:

1288

AN:

3478

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over