rs10870201

Positions:

• chr9-136362695-G-C

Variant summary

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

The NM_001080849.3(DNLZ):​c.368+294C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,158 control chromosomes in the GnomAD database, including 14,072 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 0.42 (14072 hom., cov: 34)
• Consequence: DNLZ NM_001080849.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

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]

ENSG00000289701 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNLZ	NM_001080849.3	c.368+294C>G		intron_variant		ENST00000371738.4	NP_001074318.1
DNLZ	NR_073565.2	n.402+294C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNLZ	ENST00000371738.4	c.368+294C>G		intron_variant		1	NM_001080849.3	ENSP00000360803.3
ENSG00000289701	ENST00000696169.1	n.*2552+294C>G		intron_variant				ENSP00000512460.1
DNLZ	ENST00000371739.3	c.229-515C>G		intron_variant		5		ENSP00000360804.3

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64126 AN: 152040 Hom.: 14054 Cov.: 34

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.403

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.422 AC: 64190 AN: 152158 Hom.: 14072 Cov.: 34 AF XY: 0.420 AC XY: 31224 AN XY: 74386

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.406

Alfa AF: 0.466 Hom.: 2083

Bravo AF: 0.417

Asia WGS AF: 0.406 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.78
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10870201; hg19: chr9-139257147; COSMIC: COSV52517235; COSMIC: COSV52517235;