rs11145958

Variant names:

• chr9-136360621-G-A
• rs11145958
• NM_001080849.3:c.*1391C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-136360621-G-A
• chr9-136360621-G-C
• chr9-136360621-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.*1391C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0369 in 152,146 control chromosomes in the GnomAD database, including 139 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 0.037 (139 hom., cov: 32)
  • Exomes 𝑓: 0.043 (0 hom.)
• Consequence: DNLZ NM_001080849.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 13 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNLZ	NM_001080849.3	c.*1391C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000371738.4	NP_001074318.1
DNLZ	NR_073565.2	n.1962C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNLZ	ENST00000371738.4	c.*1391C>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_001080849.3	ENSP00000360803.3
DNLZ	ENST00000371739.3	c.*1434C>T		3_prime_UTR_variant	Exon 2 of 2	5		ENSP00000360804.3

Frequencies

GnomAD3 genomes AF: 0.0369 AC: 5604 AN: 151982 Hom.: 139 Cov.: 32

Gnomad AFR AF: 0.0359

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0153

Gnomad ASJ AF: 0.0285

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0594

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.0334

Gnomad OTH AF: 0.0292

GnomAD4 exome AF: 0.0435 AC: 2 AN: 46 Hom.: 0 Cov.: 0 AF XY: 0.0556 AC XY: 2 AN XY: 36

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0238 AC: 1 AN: 42

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.0369 AC: 5614 AN: 152100 Hom.: 139 Cov.: 32 AF XY: 0.0369 AC XY: 2743 AN XY: 74362

African (AFR) AF: 0.0361 AC: 1497 AN: 41498

American (AMR) AF: 0.0152 AC: 232 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0285 AC: 99 AN: 3472

East Asian (EAS) AF: 0.127 AC: 656 AN: 5164

South Asian (SAS) AF: 0.0591 AC: 285 AN: 4824

European-Finnish (FIN) AF: 0.0440 AC: 466 AN: 10594

Middle Eastern (MID) AF: 0.00685 AC: 2 AN: 292

European-Non Finnish (NFE) AF: 0.0334 AC: 2267 AN: 67950

Other (OTH) AF: 0.0308 AC: 65 AN: 2112

Alfa AF: 0.0205 Hom.: 16

Bravo AF: 0.0342

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.053
DANN	Benign	0.66
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11145958; hg19: chr9-139255073;