dbSNP rs10781533: DNLZ:c.*855A>G (chr9-136361157-T-C) – 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.*855A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,198 control chromosomes in the GnomAD database, including 22,150 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 0.53 ( 22143 hom., cov: 34)

Exomes 𝑓: 0.50 ( 7 hom. )

Consequence

DNLZ
NM_001080849.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.736

Publications

12 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 (AMR) allele frequency at 95% confidence interval = 0.596 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.*855A>G		3_prime_UTR	Exon 3 of 3	NP_001074318.1
	DNLZ	NR_073565.2		n.1426A>G		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.*855A>G		3_prime_UTR	Exon 3 of 3	ENSP00000360803.3
	DNLZ	ENST00000371739.3	TSL:5	c.*898A>G		3_prime_UTR	Exon 2 of 2	ENSP00000360804.3

Frequencies

GnomAD3 genomes

AF:

0.534

AC:

81196

AN:

152022

Hom.:

22125

Cov.:

show subpopulations

Gnomad AFR

AF:

0.426

Gnomad AMI

AF:

0.681

Gnomad AMR

AF:

0.605

Gnomad ASJ

AF:

0.584

Gnomad EAS

AF:

0.385

Gnomad SAS

AF:

0.412

Gnomad FIN

AF:

0.525

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.601

Gnomad OTH

AF:

0.541

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.476

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)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.479

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.568

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.534

AC:

81264

AN:

152140

Hom.:

22143

Cov.:

AF XY:

0.528

AC XY:

39277

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.426

AC:

17681

AN:

41514

American (AMR)

AF:

0.605

AC:

9257

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.584

AC:

2023

AN:

3466

East Asian (EAS)

AF:

0.384

AC:

1985

AN:

5170

South Asian (SAS)

AF:

0.412

AC:

1990

AN:

4828

European-Finnish (FIN)

AF:

0.525

AC:

5559

AN:

10592

Middle Eastern (MID)

AF:

0.473

AC:

139

AN:

294

European-Non Finnish (NFE)

AF:

0.601

AC:

40863

AN:

67956

Other (OTH)

AF:

0.542

AC:

1146

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1986

3971

5957

7942

9928

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

704

1408

2112

2816

3520

<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:

0.583

Hom.:

9970

Bravo

AF:

0.535

Asia WGS

AF:

0.482

AC:

1675

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.83

(source)

DANN

Benign

0.14

PhyloP100

-0.74

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