rs10861554

Variant names:

• chr12-106076391-A-C
• rs10861554
• NM_014840.3:c.580-3548T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-106076391-A-C
• chr12-106076391-A-G
• chr12-106076391-A-T

Variant summary

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

The NM_014840.3(NUAK1):​c.580-3548T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,998 control chromosomes in the GnomAD database, including 19,901 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 0.50 (19901 hom., cov: 32)
• Consequence: NUAK1 NM_014840.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 1 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUAK1	NM_014840.3	c.580-3548T>G		intron_variant	Intron 4 of 6	ENST00000261402.7	NP_055655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUAK1	ENST00000261402.7	c.580-3548T>G		intron_variant	Intron 4 of 6	1	NM_014840.3	ENSP00000261402.2
NUAK1	ENST00000548902.1	c.187-3548T>G		intron_variant	Intron 2 of 4	4		ENSP00000448288.1
NUAK1	ENST00000553094.1	c.-24+7473T>G		intron_variant	Intron 1 of 1	4		ENSP00000446873.1
NUAK1	ENST00000549704.1	c.-171-3548T>G		intron_variant	Intron 1 of 3	4		ENSP00000449990.1

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76371 AN: 151880 Hom.: 19880 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.503 AC: 76437 AN: 151998 Hom.: 19901 Cov.: 32 AF XY: 0.509 AC XY: 37789 AN XY: 74280

African (AFR) AF: 0.467 AC: 19367 AN: 41438

American (AMR) AF: 0.541 AC: 8257 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1586 AN: 3468

East Asian (EAS) AF: 0.947 AC: 4880 AN: 5154

South Asian (SAS) AF: 0.621 AC: 2994 AN: 4820

European-Finnish (FIN) AF: 0.462 AC: 4865 AN: 10540

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.484 AC: 32883 AN: 67984

Other (OTH) AF: 0.520 AC: 1100 AN: 2114

Alfa AF: 0.480 Hom.: 20710

Bravo AF: 0.508

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.47
PhyloP100		-1.5
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: rs10861554; hg19: chr12-106470169;