rs3829109

Positions:

• chr9-136362314-G-A

Variant summary

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

The NM_001080849.3(DNLZ):​c.369-134C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 759,736 control chromosomes in the GnomAD database, including 26,258 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 0.24 (5016 hom., cov: 34)
  • Exomes 𝑓: 0.26 (21242 hom.)
• Consequence: DNLZ NM_001080849.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

Genes affected

DNLZ (HGNC:33879): (DNL-type zinc finger) Predicted to enable chaperone binding activity. Predicted to be involved in protein folding; protein import into mitochondrial matrix; and protein stabilization. Located in mitochondrion and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNLZ	NM_001080849.3	c.369-134C>T		intron_variant		ENST00000371738.4
DNLZ	NR_073565.2	n.403-134C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNLZ	ENST00000371738.4	c.369-134C>T		intron_variant		1	NM_001080849.3	P1
DNLZ	ENST00000371739.3	c.229-134C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37077 AN: 151992 Hom.: 5010 Cov.: 34

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.0551

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.234

GnomAD4 exome AF: 0.259 AC: 157164 AN: 607626 Hom.: 21242 AF XY: 0.257 AC XY: 76922 AN XY: 299738

Gnomad4 AFR exome AF: 0.163

Gnomad4 AMR exome AF: 0.388

Gnomad4 ASJ exome AF: 0.206

Gnomad4 EAS exome AF: 0.111

Gnomad4 SAS exome AF: 0.207

Gnomad4 FIN exome AF: 0.352

Gnomad4 NFE exome AF: 0.267

Gnomad4 OTH exome AF: 0.239

GnomAD4 genome AF: 0.244 AC: 37098 AN: 152110 Hom.: 5016 Cov.: 34 AF XY: 0.246 AC XY: 18258 AN XY: 74362

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.0550

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.233

Alfa AF: 0.259 Hom.: 6249

Bravo AF: 0.238

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs3829109; hg19: chr9-139256766;