rs10121646

Variant names:

• chr9-136362835-G-A
• rs10121646
• NM_001080849.3:c.368+154C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-136362835-G-A
• chr9-136362835-G-C
• chr9-136362835-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080849.3(DNLZ):​c.368+154C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0507 in 152,350 control chromosomes in the GnomAD database, including 396 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 0.051 (396 hom., cov: 35)
• Consequence: DNLZ NM_001080849.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNLZ	NM_001080849.3	MANE Select	c.368+154C>T		intron	N/A	NP_001074318.1	Q5SXM8
	DNLZ	NR_073565.2		n.402+154C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNLZ	ENST00000371738.4	TSL:1 MANE Select	c.368+154C>T		intron	N/A	ENSP00000360803.3	Q5SXM8
	ENSG00000289701	ENST00000696169.1		n.*2552+154C>T		intron	N/A	ENSP00000512460.1
	DNLZ	ENST00000893401.1		c.368+154C>T		intron	N/A	ENSP00000563460.1

Frequencies

GnomAD3 genomes AF: 0.0507 AC: 7712 AN: 152232 Hom.: 397 Cov.: 35

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0209

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.00423

Gnomad SAS AF: 0.0167

Gnomad FIN AF: 0.0114

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0507 AC: 7717 AN: 152350 Hom.: 396 Cov.: 35 AF XY: 0.0484 AC XY: 3604 AN XY: 74508

African (AFR) AF: 0.132 AC: 5484 AN: 41566

American (AMR) AF: 0.0208 AC: 319 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0403 AC: 140 AN: 3472

East Asian (EAS) AF: 0.00424 AC: 22 AN: 5190

South Asian (SAS) AF: 0.0161 AC: 78 AN: 4832

European-Finnish (FIN) AF: 0.0114 AC: 121 AN: 10624

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0215 AC: 1462 AN: 68036

Other (OTH) AF: 0.0402 AC: 85 AN: 2114

Alfa AF: 0.0277 Hom.: 273

Bravo AF: 0.0569

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.94
DANN	Benign	0.38
PhyloP100		-0.090
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10121646;

hg19: chr9-139257287;