rs10121646

chr9-136362835-G-Achr9-136362835-G-Cchr9-136362835-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNLZ	NM_001080849.3	c.368+154C>T		intron_variant		ENST00000371738.4
DNLZ	NR_073565.2	n.402+154C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNLZ	ENST00000371738.4	c.368+154C>T		intron_variant		1	NM_001080849.3	P1
DNLZ	ENST00000371739.3	c.228+652C>T		intron_variant		5

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

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.0208

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.00424

Gnomad4 SAS AF: 0.0161

Gnomad4 FIN AF: 0.0114

Gnomad4 NFE AF: 0.0215

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0250 Hom.: 84

Bravo AF: 0.0569

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.94
Dann	Benign	0.38

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: rs10121646; hg19: chr9-139257287;