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GeneBe

1-14044642-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000636203.1(KAZN):​c.92-135793T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 151,818 control chromosomes in the GnomAD database, including 30,229 homozygotes. 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: 𝑓 0.62 ( 30229 hom., cov: 31)

Consequence

KAZN
ENST00000636203.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.252
Variant links:
Genes affected
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KAZNXM_005245795.6 linkuse as main transcriptc.122-135793T>G intron_variant
KAZNXM_011541074.4 linkuse as main transcriptc.122-135793T>G intron_variant
KAZNXM_011541080.4 linkuse as main transcriptc.122-135793T>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KAZNENST00000636203.1 linkuse as main transcriptc.92-135793T>G intron_variant 5 A2
KAZNENST00000636564.1 linkuse as main transcriptc.92-135793T>G intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.617
AC:
93529
AN:
151700
Hom.:
30185
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.801
Gnomad AMI
AF:
0.407
Gnomad AMR
AF:
0.702
Gnomad ASJ
AF:
0.555
Gnomad EAS
AF:
0.701
Gnomad SAS
AF:
0.531
Gnomad FIN
AF:
0.557
Gnomad MID
AF:
0.516
Gnomad NFE
AF:
0.500
Gnomad OTH
AF:
0.628
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.617
AC:
93622
AN:
151818
Hom.:
30229
Cov.:
31
AF XY:
0.620
AC XY:
45991
AN XY:
74182
show subpopulations
Gnomad4 AFR
AF:
0.801
Gnomad4 AMR
AF:
0.703
Gnomad4 ASJ
AF:
0.555
Gnomad4 EAS
AF:
0.702
Gnomad4 SAS
AF:
0.530
Gnomad4 FIN
AF:
0.557
Gnomad4 NFE
AF:
0.500
Gnomad4 OTH
AF:
0.626
Alfa
AF:
0.525
Hom.:
9853
Bravo
AF:
0.638
Asia WGS
AF:
0.640
AC:
2223
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.2
DANN
Benign
0.53

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.

Other links and lift over

dbSNP: rs761162; hg19: chr1-14371137; API