dbSNP rs10870149: DNLZ:c.*1567C>T (chr9-136360445-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.*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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.61

Publications

23 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:

Genome browser will be placed here

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=-0.93).

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080849.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNLZ	NM_001080849.3	MANE Select	c.*1567C>T		3_prime_UTR	Exon 3 of 3	NP_001074318.1
	DNLZ	NR_073565.2		n.2138C>T		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNLZ	ENST00000371738.4	TSL:1 MANE Select	c.*1567C>T		3_prime_UTR	Exon 3 of 3	ENSP00000360803.3
	DNLZ	ENST00000371739.3	TSL:5	c.*1610C>T		3_prime_UTR	Exon 2 of 2	ENSP00000360804.3

Frequencies

GnomAD3 genomes

AF:

0.459

AC:

69652

AN:

151804

Hom.:

16265

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.440

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.450

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.643

AC:

AN:

Other (OTH)

AF:

0.400

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.459

AC:

69723

AN:

151922

Hom.:

16284

Cov.:

AF XY:

0.456

AC XY:

33875

AN XY:

74252

show subpopulations

African (AFR)

AF:

0.376

AC:

15590

AN:

41430

American (AMR)

AF:

0.544

AC:

8317

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.503

AC:

1743

AN:

3466

East Asian (EAS)

AF:

0.324

AC:

1660

AN:

5126

South Asian (SAS)

AF:

0.369

AC:

1780

AN:

4820

European-Finnish (FIN)

AF:

0.488

AC:

5143

AN:

10548

Middle Eastern (MID)

AF:

0.337

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.498

AC:

33870

AN:

67944

Other (OTH)

AF:

0.463

AC:

975

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1913

3826

5739

7652

9565

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

630

1260

1890

2520

3150

<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:

0.471

Hom.:

12534

Bravo

AF:

0.459

Asia WGS

AF:

0.415

AC:

1445

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.030

(source)

DANN

Benign

0.44

PhyloP100

-2.6

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over