Genetic Variant NM_001080849.3:c.*1391C>T (chr9-136360621-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.87

Publications

13 publications found

Variant links:

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]

DNLZ links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DNLZ	NM_001080849.3 link	c.*1391C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000371738.4	NP_001074318.1	Q5SXM8
DNLZ	NR_073565.2 link	n.1962C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNLZ	ENST00000371738.4 link	c.*1391C>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_001080849.3	ENSP00000360803.3		Q5SXM8
DNLZ	ENST00000371739.3 link	c.*1434C>T		3_prime_UTR_variant	Exon 2 of 2	5		ENSP00000360804.3		Q5SXM7

Frequencies

GnomAD3 genomes

AF:

0.0369

AC:

5604

AN:

151982

Hom.:

139

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.0556

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0238

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0369

AC:

5614

AN:

152100

Hom.:

139

Cov.:

AF XY:

0.0369

AC XY:

2743

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.0361

AC:

1497

AN:

41498

American (AMR)

AF:

0.0152

AC:

232

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0285

AC:

AN:

3472

East Asian (EAS)

AF:

0.127

AC:

656

AN:

5164

South Asian (SAS)

AF:

0.0591

AC:

285

AN:

4824

European-Finnish (FIN)

AF:

0.0440

AC:

466

AN:

10594

Middle Eastern (MID)

AF:

0.00685

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0334

AC:

2267

AN:

67950

Other (OTH)

AF:

0.0308

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

287

574

862

1149

1436

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

216

288

360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0205

Hom.:

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

(source)

DANN

Benign

0.66

PhyloP100

-1.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over