Variant rs10781533 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNLZ	NM_001080849.3 linkuse as main transcript	c.*855A>G		3_prime_UTR_variant	3/3	ENST00000371738.4	NP_001074318.1
DNLZ	NR_073565.2 linkuse as main transcript	n.1426A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNLZ	ENST00000371738.4 linkuse as main transcript	c.*855A>G		3_prime_UTR_variant	3/3	1	NM_001080849.3	ENSP00000360803	P1
DNLZ	ENST00000371739.3 linkuse as main transcript	c.*898A>G		3_prime_UTR_variant	2/2	5		ENSP00000360804

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

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.479

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.534

AC:

81264

AN:

152140

Hom.:

22143

Cov.:

AF XY:

0.528

AC XY:

39277

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.426

Gnomad4 AMR

AF:

0.605

Gnomad4 ASJ

AF:

0.584

Gnomad4 EAS

AF:

0.384

Gnomad4 SAS

AF:

0.412

Gnomad4 FIN

AF:

0.525

Gnomad4 NFE

AF:

0.601

Gnomad4 OTH

AF:

0.542

Alfa

AF:

0.585

Hom.:

8067

Bravo

AF:

0.535

Asia WGS

AF:

0.482

AC:

1675

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.83

DANN

Benign

0.14

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over