1-162510355-A-G

Position:

• chr1-162510355-A-G

Variant summary

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

The NM_175866.5(UHMK1):​c.849-2145A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,134 control chromosomes in the GnomAD database, including 6,033 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 0.25 (6033 hom., cov: 32)
• Consequence: UHMK1 NM_175866.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606

Genes affected

UHMK1 (HGNC:19683): (U2AF homology motif kinase 1) The gene encodes a serine/threonine protein kinase that promotes cell cycle progression through G1 by phosphorylation of the cyclin-dependent kinase inhibitor 1B (p27Kip1), which causes nuclear export and degradation. The encoded protein is also thought to function in the adult nervous system and the gene has been associated with schizophrenia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

UHMK1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UHMK1	NM_175866.5	c.849-2145A>G		intron_variant		ENST00000489294.2	NP_787062.1
UHMK1	NM_001184763.1	c.627-2145A>G		intron_variant			NP_001171692.1
UHMK1	NM_144624.2	c.849-2145A>G		intron_variant			NP_653225.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UHMK1	ENST00000489294.2	c.849-2145A>G		intron_variant		1	NM_175866.5	ENSP00000420270.1
UHMK1	ENST00000538489.5	c.849-2145A>G		intron_variant		1		ENSP00000446416.1
UHMK1	ENST00000545294.5	c.627-2145A>G		intron_variant		2		ENSP00000441226.1
UHMK1	ENST00000282169.8	n.1430-2145A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38473 AN: 152020 Hom.: 6034 Cov.: 32

Gnomad AFR AF: 0.0712

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.253 AC: 38473 AN: 152134 Hom.: 6033 Cov.: 32 AF XY: 0.251 AC XY: 18689 AN XY: 74350

Gnomad4 AFR AF: 0.0710

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.261

Alfa AF: 0.291 Hom.: 4587

Bravo AF: 0.246

Asia WGS AF: 0.215 AC: 750 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	0.45
DANN	Benign	0.40

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: rs7513662; hg19: chr1-162480145;