chr1-162503829-C-T

Variant names:

• chr1-162503829-C-T
• rs532796937
• NM_175866.5:c.829C>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_175866.5(UHMK1):​c.829C>T​(p.Leu277Leu) variant causes a synonymous change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: UHMK1 NM_175866.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.02

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UHMK1	NM_175866.5	c.829C>T	p.Leu277Leu	synonymous_variant	Exon 4 of 8	ENST00000489294.2	NP_787062.1
UHMK1	NM_001184763.1	c.607C>T	p.Leu203Leu	synonymous_variant	Exon 4 of 8		NP_001171692.1
UHMK1	NM_144624.2	c.829C>T	p.Leu277Leu	synonymous_variant	Exon 4 of 7		NP_653225.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UHMK1	ENST00000489294.2	c.829C>T	p.Leu277Leu	synonymous_variant	Exon 4 of 8	1	NM_175866.5	ENSP00000420270.1
UHMK1	ENST00000538489.5	c.829C>T	p.Leu277Leu	synonymous_variant	Exon 4 of 7	1		ENSP00000446416.1
UHMK1	ENST00000545294.5	c.607C>T	p.Leu203Leu	synonymous_variant	Exon 4 of 8	2		ENSP00000441226.1
UHMK1	ENST00000282169.8	n.1410C>T		non_coding_transcript_exon_variant	Exon 3 of 7	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	13
DANN	Benign	0.74

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: rs532796937; hg19: chr1-162473619;