rs10870149

Positions:

• chr9-136360445-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.*1567C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 152,004 control chromosomes in the GnomAD database, including 16,298 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 0.46 (16284 hom., cov: 32)
  • Exomes 𝑓: 0.52 (14 hom.)
• Consequence: DNLZ NM_001080849.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.61

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNLZ	NM_001080849.3	c.*1567C>T		3_prime_UTR_variant	3/3	ENST00000371738.4	NP_001074318.1
DNLZ	NR_073565.2	n.2138C>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNLZ	ENST00000371738.4	c.*1567C>T		3_prime_UTR_variant	3/3	1	NM_001080849.3	ENSP00000360803	P1
DNLZ	ENST00000371739.3	c.*1610C>T		3_prime_UTR_variant	2/2	5		ENSP00000360804

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69652 AN: 151804 Hom.: 16265 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.462

GnomAD4 exome AF: 0.524 AC: 43 AN: 82 Hom.: 14 Cov.: 0 AF XY: 0.440 AC XY: 22 AN XY: 50

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.450

Gnomad4 NFE exome AF: 0.643

Gnomad4 OTH exome AF: 0.400

GnomAD4 genome AF: 0.459 AC: 69723 AN: 151922 Hom.: 16284 Cov.: 32 AF XY: 0.456 AC XY: 33875 AN XY: 74252

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.463

Alfa AF: 0.488 Hom.: 7986

Bravo AF: 0.459

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.030
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10870149; hg19: chr9-139254897;