rs3829109

Variant names:

• chr9-136362314-G-A
• rs3829109
• NM_001080849.3:c.369-134C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 53 publications found

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]

ENSG00000289701 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DNLZ	NM_001080849.3	c.369-134C>T		intron_variant	Intron 2 of 2	ENST00000371738.4	NP_001074318.1
DNLZ	NR_073565.2	n.403-134C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNLZ	ENST00000371738.4	c.369-134C>T		intron_variant	Intron 2 of 2	1	NM_001080849.3	ENSP00000360803.3
ENSG00000289701	ENST00000696169.1	n.*2553-134C>T		intron_variant	Intron 12 of 12			ENSP00000512460.1
DNLZ	ENST00000371739.3	c.229-134C>T		intron_variant	Intron 1 of 1	5		ENSP00000360804.3

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

African (AFR) AF: 0.163 AC: 2299 AN: 14106

American (AMR) AF: 0.388 AC: 3277 AN: 8448

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 2433 AN: 11798

East Asian (EAS) AF: 0.111 AC: 2767 AN: 24848

South Asian (SAS) AF: 0.207 AC: 4025 AN: 19458

European-Finnish (FIN) AF: 0.352 AC: 8922 AN: 25346

Middle Eastern (MID) AF: 0.180 AC: 376 AN: 2084

European-Non Finnish (NFE) AF: 0.267 AC: 126277 AN: 473144

Other (OTH) AF: 0.239 AC: 6788 AN: 28394

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

African (AFR) AF: 0.168 AC: 6983 AN: 41510

American (AMR) AF: 0.344 AC: 5251 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 692 AN: 3468

East Asian (EAS) AF: 0.0550 AC: 285 AN: 5182

South Asian (SAS) AF: 0.204 AC: 984 AN: 4830

European-Finnish (FIN) AF: 0.345 AC: 3651 AN: 10576

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18478 AN: 67948

Other (OTH) AF: 0.233 AC: 492 AN: 2110

Alfa AF: 0.262 Hom.: 9006

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
PhyloP100		-0.39
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3829109; hg19: chr9-139256766;