rs11145958

Positions:

• chr9-136360621-G-A
• chr9-136360621-G-C
• chr9-136360621-G-T

Variant summary

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

The NM_001080849.3(DNLZ):​c.*1391C>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 0.0369 in 152,146 control chromosomes in the GnomAD database, including 139 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 0.037 (139 hom., cov: 32)
  • Exomes 𝑓: 0.043 (0 hom.)
• Consequence: DNLZ NM_001080849.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNLZ	NM_001080849.3	c.*1391C>T		3_prime_UTR_variant	3/3	ENST00000371738.4
DNLZ	NR_073565.2	n.1962C>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNLZ	ENST00000371738.4	c.*1391C>T		3_prime_UTR_variant	3/3	1	NM_001080849.3	P1
DNLZ	ENST00000371739.3	c.*1434C>T		3_prime_UTR_variant	2/2	5

Frequencies

GnomAD3 genomes AF: 0.0369 AC: 5604 AN: 151982 Hom.: 139 Cov.: 32

Gnomad AFR AF: 0.0359

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0153

Gnomad ASJ AF: 0.0285

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0594

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.0334

Gnomad OTH AF: 0.0292

GnomAD4 exome AF: 0.0435 AC: 2 AN: 46 Hom.: 0 Cov.: 0 AF XY: 0.0556 AC XY: 2 AN XY: 36

Gnomad4 NFE exome AF: 0.0238

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.0369 AC: 5614 AN: 152100 Hom.: 139 Cov.: 32 AF XY: 0.0369 AC XY: 2743 AN XY: 74362

Gnomad4 AFR AF: 0.0361

Gnomad4 AMR AF: 0.0152

Gnomad4 ASJ AF: 0.0285

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.0591

Gnomad4 FIN AF: 0.0440

Gnomad4 NFE AF: 0.0334

Gnomad4 OTH AF: 0.0308

Alfa AF: 0.0205 Hom.: 16

Bravo AF: 0.0342

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.053
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11145958; hg19: chr9-139255073;