rs9525029

Variant names:

• chr13-95595573-C-A
• rs9525029
• NM_198968.4:c.1538-1487G>T

Your query was ambiguous. Multiple possible variants found:

• chr13-95595573-C-A
• chr13-95595573-C-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

DZIP1 Gene-Disease associations (from GenCC):

• spermatogenic failure 47

  Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DZIP1	NM_198968.4	c.1538-1487G>T		intron_variant	Intron 15 of 22	ENST00000376829.7	NP_945319.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DZIP1	ENST00000376829.7	c.1538-1487G>T		intron_variant	Intron 15 of 22	1	NM_198968.4	ENSP00000366025.2
DZIP1	ENST00000361396.6	c.1481-1487G>T		intron_variant	Intron 14 of 21	1		ENSP00000355175.2
DZIP1	ENST00000347108.7	c.1538-1487G>T		intron_variant	Intron 13 of 20	5		ENSP00000257312.5
DZIP1	ENST00000361156.7	c.1481-1487G>T		intron_variant	Intron 12 of 19	5		ENSP00000355018.3

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

African (AFR) AF: 0.0932 AC: 3865 AN: 41476

American (AMR) AF: 0.267 AC: 4080 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3468

East Asian (EAS) AF: 0.348 AC: 1795 AN: 5160

South Asian (SAS) AF: 0.317 AC: 1515 AN: 4786

European-Finnish (FIN) AF: 0.317 AC: 3331 AN: 10518

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 23971 AN: 67940

Other (OTH) AF: 0.254 AC: 537 AN: 2112

Alfa AF: 0.314 Hom.: 9787

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
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9525029; hg19: chr13-96247827;