rs10489150

Positions:

• chr1-13927071-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000636203.1(KAZN):​c.91+33315A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,210 control chromosomes in the GnomAD database, including 1,783 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 0.15 (1783 hom., cov: 32)
• Consequence: KAZN ENST00000636203.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KAZN	XM_005245795.6	c.121+33315A>G		intron_variant			XP_005245852.1
KAZN	XM_011541074.4	c.121+33315A>G		intron_variant			XP_011539376.1
KAZN	XM_011541080.4	c.121+33315A>G		intron_variant			XP_011539382.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KAZN	ENST00000636203.1	c.91+33315A>G		intron_variant		5		ENSP00000490958	A2
KAZN	ENST00000636564.1	c.91+33315A>G		intron_variant		5		ENSP00000489835

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22552 AN: 152090 Hom.: 1785 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.0611

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.148 AC: 22552 AN: 152210 Hom.: 1783 Cov.: 32 AF XY: 0.146 AC XY: 10849 AN XY: 74408

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.0607

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.149

Alfa AF: 0.170 Hom.: 3045

Bravo AF: 0.144

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.2
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489150; hg19: chr1-14253566;