rs11112872

Variant names:

• chr12-106111556-T-G
• rs11112872
• NM_014840.3:c.241-5031A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014840.3(NUAK1):​c.241-5031A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,806 control chromosomes in the GnomAD database, including 7,434 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 0.29 (7434 hom., cov: 31)
• Consequence: NUAK1 NM_014840.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUAK1	NM_014840.3	c.241-5031A>C		intron_variant	Intron 1 of 6	ENST00000261402.7	NP_055655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUAK1	ENST00000261402.7	c.241-5031A>C		intron_variant	Intron 1 of 6	1	NM_014840.3	ENSP00000261402.2

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43760 AN: 151688 Hom.: 7423 Cov.: 31

Gnomad AFR AF: 0.0914

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.288 AC: 43795 AN: 151806 Hom.: 7434 Cov.: 31 AF XY: 0.293 AC XY: 21728 AN XY: 74176

Gnomad4 AFR AF: 0.0914

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.301

Alfa AF: 0.327 Hom.: 1111

Bravo AF: 0.273

Asia WGS AF: 0.358 AC: 1241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.76

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: rs11112872; hg19: chr12-106505334;