rs17038089

chr12-106080947-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_014840.3(NUAK1):c.579+2917G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0477 in 152,296 control chromosomes in the GnomAD database, including 254 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 0.048 (254 hom., cov: 33)
• Consequence: NUAK1 NM_014840.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.517

Genes affected

NUAK1 (HGNC:14311): (NUAK family kinase 1) Enables p53 binding activity and protein serine/threonine kinase activity. Involved in several processes, including protein phosphorylation; regulation of cellular senescence; and regulation of myosin-light-chain-phosphatase activity. Located in cytoplasm; microtubule cytoskeleton; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.092 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUAK1	NM_014840.3	c.579+2917G>A		intron_variant		ENST00000261402.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUAK1	ENST00000261402.7	c.579+2917G>A		intron_variant		1	NM_014840.3	P1
NUAK1	ENST00000548902.1	c.186+2917G>A		intron_variant		4
NUAK1	ENST00000549704.1	c.-172+2917G>A		intron_variant		4
NUAK1	ENST00000553094.1	c.-24+2917G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0477 AC: 7252 AN: 152178 Hom.: 252 Cov.: 33

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.0336

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.0337

Gnomad FIN AF: 0.00593

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0315

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0477 AC: 7266 AN: 152296 Hom.: 254 Cov.: 33 AF XY: 0.0460 AC XY: 3426 AN XY: 74476

Gnomad4 AFR AF: 0.0945

Gnomad4 AMR AF: 0.0335

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.0289

Gnomad4 SAS AF: 0.0340

Gnomad4 FIN AF: 0.00593

Gnomad4 NFE AF: 0.0315

Gnomad4 OTH AF: 0.0572

Alfa AF: 0.0352 Hom.: 64

Bravo AF: 0.0517

Asia WGS AF: 0.0410 AC: 142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
Cadd	Benign	19
Dann	Benign	0.72

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: rs17038089; hg19: chr12-106474725;