rs17038111

Variant names:

• chr12-106099109-T-C
• rs17038111
• NM_014840.3:c.361+7296A>G

Variant summary

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

The NM_014840.3(NUAK1):​c.361+7296A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0613 in 152,202 control chromosomes in the GnomAD database, including 497 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 0.061 (497 hom., cov: 32)
• Consequence: NUAK1 NM_014840.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488
• Publications: 0 publications found

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]

ENSG00000257438 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUAK1	NM_014840.3	c.361+7296A>G		intron_variant	Intron 2 of 6	ENST00000261402.7	NP_055655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUAK1	ENST00000261402.7	c.361+7296A>G		intron_variant	Intron 2 of 6	1	NM_014840.3	ENSP00000261402.2
ENSG00000257438	ENST00000774236.1	n.205-4010T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0612 AC: 9302 AN: 152084 Hom.: 495 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0389

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.00579

Gnomad FIN AF: 0.0557

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0276

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0613 AC: 9323 AN: 152202 Hom.: 497 Cov.: 32 AF XY: 0.0603 AC XY: 4485 AN XY: 74434

African (AFR) AF: 0.144 AC: 5962 AN: 41496

American (AMR) AF: 0.0389 AC: 594 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0317 AC: 110 AN: 3472

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5192

South Asian (SAS) AF: 0.00580 AC: 28 AN: 4828

European-Finnish (FIN) AF: 0.0557 AC: 591 AN: 10602

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0276 AC: 1879 AN: 68008

Other (OTH) AF: 0.0450 AC: 95 AN: 2112

Alfa AF: 0.0514 Hom.: 64

Bravo AF: 0.0634

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.7
DANN	Benign	0.54
PhyloP100		-0.49
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

Other links and lift over

dbSNP: rs17038111; hg19: chr12-106492887;