rs9525029

chr13-95595573-C-Achr13-95595573-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_198968.4(DZIP1):c.1538-1487G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,928 control chromosomes in the GnomAD database, including 6,289 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 0.26 (6289 hom., cov: 31)
• Consequence: DZIP1 NM_198968.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

Genes affected

DZIP1 (HGNC:20908): (DAZ interacting zinc finger protein 1) Predicted to enable metal ion binding activity. Involved in cilium assembly; germ cell development; and spermatogenesis. Located in cytosol; microtubule organizing center; and nucleoplasm. Colocalizes with centriole. Implicated in mitral valve prolapse and spermatogenic failure 47. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DZIP1	NM_198968.4	c.1538-1487G>T		intron_variant		ENST00000376829.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DZIP1	ENST00000376829.7	c.1538-1487G>T		intron_variant		1	NM_198968.4	P2
DZIP1	ENST00000361396.6	c.1481-1487G>T		intron_variant		1		A2
DZIP1	ENST00000347108.7	c.1538-1487G>T		intron_variant		5		P2
DZIP1	ENST00000361156.7	c.1481-1487G>T		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39939 AN: 151810 Hom.: 6285 Cov.: 31

Gnomad AFR AF: 0.0932

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.263 AC: 39951 AN: 151928 Hom.: 6289 Cov.: 31 AF XY: 0.263 AC XY: 19492 AN XY: 74210

Gnomad4 AFR AF: 0.0932

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.254

Alfa AF: 0.324 Hom.: 7755

Bravo AF: 0.252

Asia WGS AF: 0.291 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	7.5
Dann	Benign	0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9525029; hg19: chr13-96247827;